Clark moved into first place in the school's record book with 23 TD passes in a season and 42 in a career.
Penn State (10-2, 6-2 Big Ten) now must wait to learn of its postseason destination. The Nittany Lions have a shot at getting a BCS berth. The conference's automatic bid goes to Ohio State.
Michigan State (6-6, 4-4) also is bowl-bound.
Evan Royster gained 114 yards on 13 carries for Penn State, which pulled away in the third quarter after the score was tied 7-7 at halftime.
Kirk Cousins completed 16 of 28 passes for 155 yards and a touchdown for the Spartans. He was intercepted twice, setting up short Penn State scoring drives.
Penn State is assured of back-to-back seasons of at least 10 wins for the first time since 1993-94, but the Nittany Lions lost any chance to share the Big Ten championship before kickoff. Ohio State, which had already clinched the BCS berth, claimed the crown outright by beating Michigan earlier in the day.
The Nittany Lions have a shot at an at-large BCS bid, but Iowa - which beat Penn State earlier this season - finished with an identical 10-2 record. Only two teams from any conference can play in the BCS.
Orange Bowl representatives were at Saturday's game. Penn State could be a prime candidate for the Capital One Bowl or the Outback Bowl if it gets left out of the BCS.
Michigan State will be headed to a bowl for the third straight season for the first time since 1995-97. But the Spartans' defense was shredded by Penn State after halftime.
Penn State grabbed a 14-7 lead just over a minute into the half with the help of a trick play. Wide receiver Curtis Drake took a handoff and rolled right, throwing a 14-yard touchdown pass to Andrew Quarless in the back of the end zone.
It capped a 55-yard, three-play drive aided by a roughing the passer penalty.
Penn State increased its lead to 21-7 midway through the third quarter. Clark rolled to his right, planted and threw back across the field to the left sideline - finding Joe Suhey all alone for a 30-yard TD pass.
Penn State's Nick Sukay intercepted Cousins' pass on the next series, setting up the Nittany Lions at the Michigan State 32. Clark fired a TD pass to Graham Zug on the very next play, giving Penn State a 28-7 lead with 5:22 left in the third.
The Land Grant Trophy - a 4-foot-tall, 50-pound hunk of wood adorned with a Nittany Lion, Spartan and other images - stays with Penn State after Saturday's victory.
The trophy was created when Penn State joined the Big Ten in 1993. Penn State and Michigan State are the nation's pioneer land grant universities.