"It's been a long time since we got our butts whipped like that," Navy coach Ken Niumatalolo said. "And that starts with me. It was a thorough beating."
The Midshipmen played without fullback Alexander Teich, their leading rusher, who was held out of the game by Niumatalolo for disciplinary reasons.
"Any time you lose one of your star players, it affects the team," Navy quarterback Kriss Proctor said. "But this was a team loss, not a one-player loss."
Navy's Delvin Diggs ran for two touchdowns, and Proctor added 123 rushing yards. But Navy's defense was unable to contain Southern Miss quarterback Austin Davis and its offense came away empty on two early scoring opportunities.
It was the most points allowed by Navy since a 65-19 home loss to N.C. State on Sept. 7, 2002. Southern Miss, meanwhile, topped 50 points for the second time in four games and is averaging 48 points a game during their winning streak.
The Midshipmen amassed 421 rushing yards, but paid for squandering long drives on their first two possessions. Even it had an early 144-0 edge in offensive yardage, Navy was down 7-0.
Davis completed 21 of 23 passes for 283 yards and three touchdowns, and added 75 yards and a touchdown on 12 carries.
"Since I've been there, I think this is as good as we've executed from the start to the finish," Davis said. "I thought we didn't let up in the second half. We played just as well in the second half as we did in the first."
Jeremy Hester rushed for 118 yards and a score and Tracy Lampley ran for two touchdowns for the Golden Eagles (5-1), who now get a bye week before beginning a stretch of six straight Conference USA games.
Though Southern Miss couldn't completely corral Navy's vaunted running attack, the Golden Eagles didn't let the Midshipmen grind out so much yardage that they were playing from behind early on.
"I knew they could score," said Southern Miss coach Larry Fedora. "But I thought we could make them snap it and score and eat some clock. They were getting too many big plays and when they are doing that offensively, you have to answer."
Navy (2-3) rallied for 28-second half points but lost a third consecutive game for the first time in four seasons under Niumatalolo, surrendering a season high in points.
The Midshipmen drove to the Golden Eagles' 7-yard line on the game's opening drive, but Southern Mississippi's Khyri Thornton blocked Jon Teague's 29-yard field goal try and Marquese Wheaton scooped up the loose ball, returning it 79 yards for a touchdown.
Navy moved to the Southern Miss 1 on the ensuing drive, but failed on three tries to punch the ball across for a score. Tim Green stuffed Proctor's fourth-down keeper attempt.
"That was basically just a bend-but-don't-break attitude that we had given up some big plays on those first two drives," Southern Miss linebacker Ronnie Thornton said. "We decided to buckle down down there in the deep end."
The Golden Eagles offense didn't touch the ball until 3:59 remained in the opening quarter, and Davis directed a 99-yard scoring drive capped by Hester's 3-yard scamper up the middle for a 14-0 lead.
"When you have a 14-point swing like that at the start of the game, it is a huge play," Proctor said. "We have to find a way to score."
Lampley's 4-yard scoring run put the Golden Eagles up 21-0 with 11:18 remaining in the first half.
Davis found Ryan Hanks uncovered in the end zone for a 5-yard scoring pass and a 28-8 lead 7:32 before halftime.
Navy responded with a six-play, 70-yard drive culminating in John Howell's 1-yard right-side run. But Southern Miss took a 35-7 lead on a 5-yard touchdown pass from Davis to Ryan Balentine.
Davis finished the first half 13 for 14 for 191 yards.
Proctor needed only 57 seconds to move Navy 74 yards early in the second half, leading Brandon Turner over the middle for a 43-yard touchdown pass to trim the deficit to 35-14.
But Davis threw his third scoring pass of the afternoon, a 10-yard strike to Kelvin Bolden in the back of the end zone, for a 42-14 Southern Miss lead.
Diggs scored on a 1-yard run, but Southern Miss used a trick play - an 18-yard pass from Quentin Pierce to Collin Jarbo - to increase its lead to 49-21. Proctor then threw a 27-yard TD to Gee Gee Green with 40 seconds left in the third quarter.
Lampley's second touchdown run made it 56-28 early in the final quarter. Diggs then scored from 7 yards out for Navy.
Davis' 1-yard run with 5:18 left concluded the scoring.
"We were scrambling to catch up," Niumatalolo said. ''We couldn't finish in the red zone. But there is no alternative for us. We have to look in the mirror and find a way to get better.''