Harbaugh questioned two non-calls in the final series when the 49ers failed to convert with a first and goal as they looked to find receiver Michael Crabtree with the game on the line.
"There's no question in my mind that there was a pass interference and then a hold on Crabtree on the last one," said Harbaugh.
Harbaugh also was unhappy about what transpired on the game's penultimate play. After the Ravens attempted to run out the clock before punting in the final seconds, Harbaugh questioned the failure of officials to call holding as Ravens punter Sam Koch ran around in the end zone to eat up time before taking a safety with four seconds to play.
I still haven't gotten an explanation on the safety. It was obviously the intent of the Ravens to tackle and hold... but not one holding flag came out," Harbaugh said. "I realize I am on the side of the 49ers, I'm the coach and probably have some bias there but in my mind I thought it was obvious, but that's not the way they saw it."
Harbaugh also protested the decision to penalize his cornerback Chris Culliver for pass interference, allowing the Ravens to make a crucial first down after Joe Flacco had thrown an incomplete pass on third down with the score 31-29.
"I didn't think that was an interference," said Harbaugh.
But the 49ers coach was also critical of his players, who paid the price for turnovers and penalties.
"We want to handle this with class and grace. We had several opportunities in the game. We didn't play our best game. Ravens made a lot of plays. Our guys battled back to get in it. We competed and battled to win," he said.
49ers make Super Bowl history
The 49ers became the first team in Super Bowl history to have a 300-yard passer, a 100-yard rusher and two 100-yard receivers in the same game.
Quarterback Colin Kaepernick threw for 302 yards, running back Frank Gore had 100 yards rushing, wide receiver Michael Crabtree had 109 yards receiving and tight end Vernon Davis had 104 yards receiving.
Davis tied the Super Bowl record for most receiving yards by a tight end.
Kaepernick completed 16 of 28 passes, with six receptions going to Davis and five to Crabtree. Averaging 18.9 yards per completion and 10.8 yards per pass, Kaepernick had long completions of 32 and 31 yards, three completions of 29 yards, another of 28 yards and two of 24 yards.
Gore set a franchise record for most rushing yards in a Super Bowl game and also had his fourth rushing touchdown of this postseason among his 19 carries.
Kaepernick rushed for 62 yards on seven carries, and his 15-yard scoring run that brought the 49ers within 31-29 in the fourth quarter was the longest touchdown run by a quarterback in Super Bowl history.
MVP Flacco no ordinary Joe
Joe Flacco won't have to do much negotiating after this.
The low-key Ravens quarterback put off talks on a new contract until after the season. Now when he and the Ravens sit down, all he'll have to do is show off his Super Bowl MVP trophy.
''It's cool,'' Flacco said Sunday night. ''We just won a Super Bowl. That's the last thing I'm concerned about. But (owner Steve Bisciotti) did let me know that if that day came, I could go beat on his desk and really put it to him.
''So that's exactly what I'm going to do.''
Flacco capped a perfect postseason, throwing three touchdown passes in the first half to stake the Ravens to a lead they would never relinquish. When the 49ers made a furious comeback after a power outage interrupted the third quarter for 34 minutes, Flacco was cool and controlled.
Let the Niners make their run, he almost seem to say, we'll hold our own.
''You've seen these guys do it,'' Flacco said. ''They have the ability to score and to score quickly, and that's what they did.''
Flacco finished 22-of-33 for 287 yards. He didn't throw an interception – didn't throw one the entire postseason, to be precise. His 11 touchdowns in the postseason matched a record set by Joe Montana.
''That's pretty cool,'' Flacco said. ''Joe Montana is my favorite quarterback so it's pretty cool.''
So is being the Super Bowl MVP.
Truth is, the trophy could have gone to a number of the Ravens. But Flacco is happy to have it.
''They have to give it to one guy,'' Flacco said, laughing. ''I'm not going to complain that I got it.''
Odds of Niners winning 2014 Super Bowl: 8-1
So now that the Ravens are NFL champs, what are the odds they'll do it again?
According to sports books in Las Vegas, 14 to 1.
Casinos put up lines for next year's championship immediately following the Super Bowl.
The 49ers are actually a bigger favorite to win it all next year, 8 to 1, tied with the Denver Broncos. New England is the overall favorite.
Kap: Last play was an audible
Quarterback Colin Kaepernick came just short of leading the 49ers to an unprecedented Super Bowl comeback.
But with three chances to take the lead needing 5 yards for a touchdown, Kaepernick had three straight incompletions.
All three passes were intended for wide receiver Michael Crabtree, who got tangled up with a defender on the final play. No holding was called – Harbaugh screamed from the sideline and signaled for a penalty.
Kaepernick's off-balance throw under pressure on fourth down sailed through the end zone. He lowered his head slightly and walked slowly off the field.
''That wasn't the original option,'' Kaepernick said. ''It's something I audibled to at the line based on the look they gave us.''
Power outage caused by ‘abnormality'
Officials say the Superdome power outage during the Super Bowl was triggered by an ''abnormality'' in the power system.
That triggered an automatic shutdown and forced backup systems to kick in, officials said about two hours after the Ravens beat the 49ers.
But officials still aren't sure what caused the initial problem.
A joint statement from Entergy New Orleans, which provides power to the stadium, and Superdome operator SMG gives a chain of events.
The problem started at the spot where Entergy feeds power into the stadium's lines, and occurred shortly after Beyonce's halftime show with extravagant lighting and video effects.
''A piece of equipment that is designed to monitor electrical load sensed an abnormality in the system,'' the statement said. ''Once the issue was detected, the sensing equipment operated as designed and opened a breaker, causing power to be partially cut to the Superdome in order to isolate the issue. ... Entergy and SMG will continue to investigate the root cause of the abnormality.''
The FBI has ruled out terrorism. The concourses didn't go totally dark thanks to auxiliary power.
49ers quick hits
--- Vernon Davis registered his fourth 100-yard receiving game in five career postseason games. He's now tied with Keith Jackson for most 100-yard receiving games by a tight end in NFL postseason history.
--- Davis joined Arizona wide receiver Larry Fitzgerald as the only players in NFL postseason history to register four 100-yard receiving games in their first five career playoff games.
--- Defensive tackle Ray McDonald notched his first sack of this postseason, bringing down Ravens QB Joe Flacco. McDonald now has 3.5 career postseason sacks.
--- Linebacker Ahmad Brooks brought down Flacco for his first sack of the postseason. He now has 2.0 career postseason sacks.
--- Cornerback Tarell Brown striped Ravens running back Ray Rice and recovered the loose ball in the third quarter. It marked Brown's first career postseason FF and FR. The takeaway led to a 34-yard field goal by K David Akers.
--- With three field goals and two PATs, Akers now has 175 career points in the postseason, the second-most in NFL history behind Adam Vinatieri's 196 points.
--- Akers has now scored a point in all 24 playoff games in which he has appeared, the second-longest streak in NFL history behind Vinatieri's 25-game streak.
--- First-team All-Pro defenders Patrick Willis, NaVorro Bowman and Dashon Goldson combined for 28 tackles. Willis led the way with a game-high 10 stops, while Bowman and Goldson each had nine, with two of Bowman's tackles resulting in losses behind the line of scrimmage.