Oregon (27-10) trailed the Highlanders 3-1 after five innings, but knotted the score in the sixth before taking a three-run lead in the seventh.
Left fielder Tyle Baumgartner led off the inning with a solo home run to right field. The ball which went over the foul pole, was initially ruled foul by the first base umpire, but was overturned following a huddle of the crew.
"I asked them to get together and get it right, and I think they did," Oregon coach George Horton said.
Horton, who admits he had a poor angle on the call, rushed out of the dugout to meet with first base umpire Mike Whitty, after witnessing Baumgartner's reaction.
"I think it was right on top. It was kind of a skyscraper, so it was a tough one for the field umpire to see," he said. "Off the bat it looked like it was going to hook foul, but it stayed just fair."
Mitchell Tolman smacked a double down the left field line, and acted as the tying run after J.B. Bryant came through with a pinch hit RBI single.
Oregon followed up the two-run sixth with three in the seventh, with most of the action coming off of Baumgartner and Kyle Garlick doubles.
Garlick's shot to deep center scored two runs and acted as the game's go-ahead run.
"I got to 3-0 [count] and [hitting coach] Wasikowski gave me the green light," Garlick said. "3-0 is automatic take unless he gives you the green light.
"It's usually only in RBI situations, so I was pumped when he game me that."
The Ducks were fortunate to add an insurance run on as Shaun Chase sacrifice bunt the sacred Garlick, as UC-Riverside would rally in the ninth.
Oregon closer Jake Reed allowed a two-out Francisco Tellez two-run homer, which created some angst in the crowd.
But Reed got the next batter, Nick Vilter, to ground out on the next at-bat.
"I was most impressed with how he threw to the next hitter," Horton said. "That's some mental toughness that a closer has to have, you have to short memory to get back to the next hitter some time."
The game's final out drew some controversy, as Highlander manager Doug Smith ran down the umpire crew to argue that first baseman A.J. Balta's foot was off the bag.
Freshman Trent Paddon made his Oregon starting debut and managed four innings of work.
Paddon is replacing fellow frosh Matt Krook for the final weekend spot as Oregon awaits word on his health.
Paddon asserted himself decently enough, allowing three runs on six hits in those four innings.
"I had a couple more weapons than just using my fastball," Paddon said of his off-speed pitches, "But I think I need to work a little more on location. A couple of times I got it in, but other times I left it over the plate and they got some big hits off of those pitches."
Horton says Paddon will remain in the rotation next weekend.
Aaron Payne stole second base in the bottom of the fourth. It was his 40th career SB, tying Donnie Reynolds for the school's careers best. Payne scored the game's first run on a Mitchell Tolman single two pitches later.
Middle of the lineup hitters Baumgartner, Tolman and Garlick each had two hits.