The Wildcats end 2012 with a record of 8-3 and reached the postseason for the 12th time in school history.
The Cougars improved to 9-3 and will move on to the national quarterfinals next week, with its next opponent to be determined.
The Wildcat defense was solid all day long, holding the USF offense to just 3.1 yards per carry on 41 carries and 126 yards.
Seniors Scott Schrag and Ryder Werts each had double-digit tackles, as Schrag led the Wildcats with 16 and Werts had 15 with a sack and 2.5 tackles for loss.
St. Francis scored on its first possession with 11:14 to go in the first quarter on an 11-yard pass play from Josh Miller to Colin Harruff.
Emerson Ueber missed the extra-point and USF led early, 6-0. On the Wildcats next possession, Baker marched down the field 60 yards on 16 plays and ate up 7:27 on the clock. But senior kicker Steven Stewart just missed a 38-yard field goal attempt.
The Wildcat defense held USF to a three and out on its next possession, Baker then put itself in field goal range for the second straight time and again Stewart missed a 40-yard field goal to give St. Francis the ball back.
The Cougars scored next on a 26-yard field goal by Ueber to go up 9-0. The Wildcats responded with its first score of the day on a one-yard touchdown score by Jesse Schultz, as he leapt in the air above the line of scrimmage and landed in the end zone.
USF followed that up with one of its best drives of the game marching down the field 79 yards on 12 plays and scored a touchdown on a 13-yard touchdown scamper by quarterback Josh Miller.
Just before halftime, Dylan Perry had a big return of 44 yards to the 50-yard line and quarterback Sam Vossen then threw a perfect ball right down the middle of the field to senior Kyle Bolton for a 23 yard pass play to set up a field goal try by Stewart.
Stewart stepped up and nailed a 44-yarder to put Baker within six points at the break, 16-10.
Dillon Baxter had just 26 yards on 10 carries in the first half, but turned it on in the second carrying the Wildcats on his back down the stretch
USF punted on its first possession out of halftime and Bryan Williams saw his first action of the game on Baker's first possession of the second half with a 21-yard punt to give USF the ball back at its own 38 yard line.
Baker then forced a turnover in the red zone as Emmerson Clarke came in and blew up Antoin Campbell and forced a fumble at the Baker 12 yard line and Andre Jolly picked up the ball for Baker taking it to the Baker 14.
But Vossen then fumbled for the Wildcats and gave it right back to the Cougars. Ueber then connected on a 24-yard field goal to give St. Francis the 19-10 lead.
The Wildcats then let Baxter carry the ball eight times on its next possession and the junior from Chula Vista, Calif., ran for 48 yards on those eight carries and ended the drive with a five-yard touchdown. Baker now trailed 19-17 with 6:35 to go in the game.
The Cougars added to its lead with 3:58 left on a Ueber 22-yard field goal to put USF up, 22-17.
On Baker's next drive the Wildcats made it to the USF 48-yard line, until Vossen threw an interception into the arms of Jamael Green and USF never gave the ball back and took home its 17th-straight home win in the NAIA FCS Playoffs.
Baxter finished the day with 102 yards rushing on 22 attempts and Vossen had a solid day going 17-of-29 for 203 yards.
Bolton led the team with 78 yards receiving and Reggie Harris added 48 yards receiving. Sophomore Jolly ended the season with 16 sacks leading the NAIA.