After the 25th-ranked Tigers scored on the opening possession of overtime, their defense delivered, too. Missouri sacked a backpedaling C.J. Bacher, forcing a fumble that left Northwestern with fourth-and-goal from the 32-yard line.
Bacher's desperation heave into the end zone was knocked down, and Daniel rushed off the sideline with his teammates to celebrate.
The win gave Missouri (10-4) double-digit victories in consecutive seasons for the first time in school history. The No. 22 Wildcats (9-4) fell to 1-6 in bowl games, with their only win coming in their first bowl appearance in 1949.
Playing his final college game, Daniel overcame three interceptions to lead the Tigers back from a three-point deficit in the fourth quarter.
"I've never had something like that," Daniel said. "I was just glad I could help the team in the end. I was obviously hurting the team very bad in the beginning."
Jeff Wolfert made three field goals, including a 37-yarder with 2:49 remaining that tied it 23-all. But he missed a 44-yard attempt that could have won it for Missouri as time expired.
"We were all a little stunned," Pinkel said. "We got it together quickly."
Daniel, who finished fourth in 2007 Heisman Trophy voting, matched a season high with his three interceptions. He was 27-of-44 for 200 yards and two touchdown passes.
"He had the adversity during the game," Missouri coach Gary Pinkel said. "What defines him is he fought back from it with his teammates."
The speedy Maclin, a first-team All-America as an all-purpose player, also returned a punt 75 yards for a score that tied it at 10 in the second quarter.
Bacher threw for 304 yards and equaled an Alamo Bowl record with three touchdown tosses. His 23-yard scoring pass to Ross Lane in the back of the end zone gave Northwestern a 23-20 lead at the end of the third.
The score came after Brad Phillips grabbed an interception and returned it to the 24.
After the Tigers tied it, Northwestern had a chance to drive for a go-ahead score, but Bacher's pass on third-and-3 with less than two minutes remaining fell incomplete.
"We didn't have a moral victory tonight, OK," Northwestern coach Pat Fitzgerald said. "We're very disappointed that we lost the game. We fought hard and we fought valiantly, but there are not moral victories."
A 43-yard field goal by Wolfert made it 20-16 Missouri with just under four minutes remaining in the third. That score was set up by an interception and 22-yard return by Brock Christopher.
Danario Alexander gave Missouri a 17-16 lead - its first of the game - with about seven minutes remaining in the third quarter on an 11-yard touchdown pass from Daniel.
Bacher found Rasheed Ward for a 46-yard touchdown pass on the first drive of the second half. Villarreal's extra point bounced off the right upright to leave the score at 16-10 Northwestern.
Maclin, who leads the NCAA in all-purpose yards, tied it 10-all with his 75-yard punt return for a touchdown just before halftime. He bolted through the first wave of defenders before getting a good block and zooming past punter Stefan Demos, who had an angle on him but tripped.
It was the first punt return TD this season for Maclin.
Things started rough for Daniel when his pass was tipped and intercepted by Brian Peters on Missouri's first drive. Northwestern took advantage of that mistake when Bacher found a wide-open Eric Peterman streaking down the middle of the field for a 35-yard touchdown to put the Wildcats up 7-0 early in the first quarter.
Northwestern got a 21-yard field goal by Villarreal to make it 10-3 in the second.
Daniel's second interception came on an ill-advised throw under heavy pressure from David Arnold in the second quarter. Defensive end Corey Wootton, 6-foot-7, made a diving grab just before the ball would have hit the turf.
Northwestern came away empty, though, when Villarreal's 47-yard field-goal attempt sailed wide left.
Wootton, who also had a sack, appeared to injure his right leg with about four minutes remaining and did not return.
Missouri's first points came on a 31-yard field goal by Wolfert early in the second quarter.