Penn State forced four turnovers for the second straight game. Navy now has six lost fumbles in its first two games after losing nine all of last year.
Those turnovers were costly for Navy, which otherwise was able to keep up with Penn State's new-fangled offense modeled after the attack O'Brien coordinated while he was with the New England Patriots. Navy outgained Penn State in total offense (371-341) and first downs (22-16) and held the ball for 36 minutes.
But much of Navy's yardage came in the fourth quarter with the game well in hand for Penn State. Another bright spot for the Midshipmen came on fourth downs, when Navy converted 5 of 8 chances.
Matt McGloin threw for 231 yards and four touchdowns and rookie coach Bill O'Brien got his first career victory.
The Nittany Lions (1-2) rolled to the morale-boosting win following two draining losses to open a season of change in Happy Valley. Penn State hadn't won a football game since last Nov. 19 at Ohio State. Scandal marred Penn State's offseason.
The win over Navy gave Penn State something to celebrate.
Allen Robinson torched the Midshipmen's porous secondary for three touchdowns and 136 yards on five catches, and Penn State's four turnovers included Mike Hull's 74-yard fumble return to make it 34-0 in the fourth quarter.
The seven penalties for 41 yards didn't help Navy, either.
"It's uncharacteristic of us. We didn't play well. I didn't coach well," Niumatalolo said. "We've got to play mentally perfect to have a chance against a team like Penn State. We didn't come close, not even close."
Greene's 12-yard touchdown run with 10:03 left at least snapped the shutout.
On a play fake, McGloin scrambled right and found tight end Jesse James in the end zone for a 2-yard touchdown catch and a 7-0 lead on the game-opening drive. More than five minutes later, McGloin hit Robinson with a pass at about the 10, but the sophomore two-stepped around defensive back Tra'ves Bush to jog untouched into the end zone for a two-touchdown lead.
Linebacker Gerald Hodges thwarted Navy's next drive into Penn State territory, intercepting an underthrown pass into the flat at the 10 by Navy quarterback Trey Miller, who was flushed out of the pocket under pressure. That turnover set up a 14-play, 90-yard drive that culminated with another Robinson touchdown catch, this one from two yards out.
Miller, who had both feet heavily taped, injured an ankle in the 50-10 loss to the Irish. Appearing to walk with a slight limp, Miller was ineffective in the pocket, rushing 18 times for 21 yards and going 6 of 13 passing for 17 yards and an interception.
"I've just got to take care of the football," Miller said. "We hurt ourselves today."
In came freshman backup quarterback Keenan Reynolds in the third quarter, who deftly led Navy's triple-option offense from its own 21 to the Penn State 26 before another mistake - this time a fumble by Noah Copeland at the line of scrimmage.
Hull emerged out of a swarm of blue shirts and raced down the middle of the field untouched 74 yards for a 34-0 lead.