Stony Brook quarterback Kyle Essington, who has thrown 22 touchdown passes, was declared out for the game with a thigh injury. Lyle Negron, who attempted five passes in the regular season, got the start.
Negron only needed to throw the ball three times in the first half, in which the Seawolves owned a 14-0 lead.
Both touchdowns were scored by 5-foot-10, 210-pound senior Miguel Maysonet, who entered the game the leading FCS rusher with 1,721 yards.
If ever a tone were set, it was on that first drive where Stony Brook went 98 yards on 21 plays, with Maysonet doing the finishing touch on a 1-yard scoring run. The Seawolves drive took 12 minutes and 43 seconds.
And if Maysonet weren't enough to contend with, Villanova had trouble with University of Iowa transfer Marcus Coker, a 6-0, 230-pound junior who combines speed and power.
While Maysonet gained 160 yards on 25 carries and scored two touchdowns, Coker added 107 yards on 29 carries.
The Seawolves pounded behind a jumbo offensive line that included tackles Scott Hernandez (6-6, 300) and Michael Bamiro (6-8, 345).
Stony Brook continued moving the ball on its first third quarter possession but the momentum momentarily switched when the Wildcats' Craig James forced a Coker fumble that was recovered by Ronnie Akins at the Villanova 43.
The Wildcats were able to get a 41-yard Mark Hamilton field goal, cutting the margin to 14-3 with 7:59 left in the third quarter.
Stony Brook answered on the next possession with a 37-yard field goal by Wesley Skiffington and that was only the beginning.
On the ensuing kickoff, Villanova never fielded the ball and Stony Brook's Naim Cheeseboro recovered on the Wildcats' 25-yard line.
Skiffington kicked a 29-yard field goal to extend the lead to 20-3 with 13:33 left.
Villanova was forced to gamble on the next series, electing not to punt on a fourth-and-3 from its own 32-yards line. John Robertson's intended pass to Norman White was incomplete.
Skiffington missed a 45-yard field goal, with 10:31 left, still giving the Wildcats a glimmer of hope.
Robertson scored on a 21-yard run with 6:57 left to cut the margin to 20-10. On that play Robertson became the first Villanova quarterback to rush for more than 1,000 yards in a season. That gave him 1,011 yards.
Instead of a traditional onsides kick, Chris Goff kicked a high ball that Maysonet easily fair caught on the Stony Brook 34.
Villanova's defense forced a punt, but then Stony Brook's Davonte Anderson sealed matters on an interception with 4:15 left.
Contact Marc Narducci at email@example.com or @sjnard on Twitter.