Penn State (3-1) held the Eagles (2-2) to 68 on the ground - 221 below its season average - and forced three first-half turnovers. Nick Sukay's interception late in the half set up the second of McGloin's scoring strikes, a 5-yarder to receiver Derek Moye for a 17-0 lead.
It surely pleased the 84-year-old Paterno, who paced the sideline in the first half for the first time this season before returning to the press box after halftime with his team up comfortably. The Hall of Famer spent the first three games entirely upstairs while recovering from injuries suffered from an accidental collision in practice Aug. 7.
The defense contained Eastern Michigan, though the injury news wasn't good on the field for Penn State. Linebacker Michael Mauti, the team's leading tackler, limped into the locker room in the first quarter with an ice pack strapped to his left knee.
Later, Paterno said Mauti was likely out for the year after injuring his ACL.
The announced crowd of 95,000 at Beaver Stadium went silent while trainers looked at cornerback D'Anton Lynn's neck and upper back late in the third quarter. Lynn was strapped to a backboard as a precaution and carted off the field late in the third quarter. A team spokesman said Lynn had movement in his extremities and was taken to Mount Nittany Medical Center.
Lynn had "burners" down his arms and was breathing heavily after the hit, defensive coordinator Tom Bradley said after the game.
It dampened the mood late in what had been a nice afternoon for the Nittany Lions.
"I feel sorry for the kids," Paterno said. "It does take a little out of the win, but that's the way it goes.
Wearing his familiar khakis and jet-black sneakers, Paterno looked back in his element Saturday as he paced the sideline slowly and found coaches or players to pester.
There wasn't much to complain about in the end. Whether Paterno was upstairs or on the field, his Nittany Lions flustered Eastern Michigan. The Eagles were held to two field goals by Kody Fulkerson.
Defensive tackle Devon Still led the push up front and Penn State sacked Eastern Michigan quarterback Alex Gillett three times alone in the first half. The opportunistic defense held tailback Javonti Greene to nine carries for 22 yards, more than 90 below his season average.
It was more than enough cushion to give Penn State's struggling passing game and two-quarterback system a chance to get back on track. The Nittany Lions scored through the air for the first time all season, and both McGloin and sophomore Rob Bolden got in on the fun.
Bolden started the game. He finished 7 of 13 passing for 115 yards an interception, plus a screen to speedy receiver Devon Smith that turned into a 71-yard touchdown pass for a 24-0 lead a minute into the second half. It was Smith who accidentally ran into Paterno after running a route in practice to give the head coach his latest ailments.
Saturday, Smith impressed his coach after finishing with three catches for 104 yards.
Moye finished with six catches for 65 yards and two scores. Both were from McGloin, who was 14 of 17 passing for 220 yards after entering in the second quarter. He and Bolden alternated from there until third-stringer Shane McGregor took over in the fourth quarter with Penn State up by 28 points.
Not only did McGloin have the better day statistically, but the offense seemed to run smoother Saturday with the junior calling the signals.
Gillett didn't have as good a time, though he did have Eastern Michigan moving at times through the air. That was a mild surprise given Eastern Michigan had the sixth-best rushing attack in the FBS entering Saturday.
Gillett finished 18 of 31 passing for 202 yards, and ran for 22 yards on 15 carries. The Eagles finally got on the board with 11:50 left on Fulkerson's 21-yard field goal.
