In State College, Pa., John Shaffer passed for one touchdown and Kevin Woods ran for another.
Penn State is 3-0 and East Carolina 2-1.
Penn State took a 7-0 lead 6:54 into the first period on a four-yard pass from Shaffer to Eric Hamilton. East Carolina cut it to 7-3 late in that period on Jeff Heath's 34-yard field goal.
In the second period, Woods ended a four-play, 44-yard drive with a 24-yard run that gave the Nittany Lions a 14-3 lead.
But the Pirates cut it to 14-10 with 6:16 left in the third period when fullback Anthony Simpson ran eight yards to end an 11-play, 64-yard drive.
They muffed a chance to go ahead on their next possession, after driving 71 yards to the Penn State 20. Simpson gained five yards on two carries, then Tony Baker ran to the nine, where he fumbled and Penn State cornerback Duffy Cobb recovered.
Penn State made it 17-10 with 3:49 left in the game on Massimo Manca's 38-yard field goal. Those were the first points East Carolina had given up in the second half this season.