MINNEAPOLIS — Minnesota took an 11-point deficit into halftime of the homecoming game against a Purdue team the Gophers were favored to beat by nearly two touchdowns.

That here-we-go-again, just-when-this-was-getting-good feeling spread among the fans. Coaches and players, though, saw this differently. Calm confidence founded a comeback, and Minnesota finished the afternoon alone in first place in the Big Ten West Division.

David Cobb rushed for 194 yards and a touchdown, Ryan Santoso kicked a 52-yard field goal with 4:59 left for the lead and the Gophers beat the Boilermakers 39-38 for their first 3-0 start in conference play since 1990.

Cedric Thompson had two interceptions for Minnesota (6-1, 3-0), including a diving pickoff of Austin Appleby with 2:28 remaining to seal it.

“My first year, once we were down, we were like, ‘It’s over,”’ Thompson said. “But going into the half, us being down, we had no worries at all. We said we were going to fight and go out there and win this game.”

This was the first time in 23 games under coach Jerry Kill that the Gophers rallied from behind to win. Purdue led 31-20 with 304 total yards at the break.

“When I walked into the locker room, I said, ‘Hey men, this is going to define who you are,”’ Kill said.

The definition for now is Big Ten contenders. With the West wide open, the Gophers badly needed this game and next week’s at Illinois to stay relevant in the race facing a daunting November schedule: Iowa and Ohio State followed by trips to Nebraska and Wisconsin.

A one-point win over the Boilermakers, who are 1-11 in the conference under coach Darrell Hazell and lost 38-17 at home this year to Central Michigan, won’t do much for Minnesota’s resume come time for bowl game bids. But it did ensure the Gophers are eligible — and deepen their belief they can rally when they need to.

“It’s just a start. So it depends on how we finish,” said Cobb, who passed the 1,000-yard mark for the second straight season.

Appleby threw three first-half touchdown passes for the Boilermakers (3-5, 1-3), but he was only 4 for 10 for 18 yards in the second half. Raheem Mostert rushed for 115 yards on just five carries and Akeem Hunt added 98 yards on 17 attempts, but another upset bid fell short. Last week, Purdue had the ball in the closing minutes trailing Michigan State by seven before the Spartans scored on an interception return.

“I think we’re on the verge of a breakthrough,” wide receiver Danny Anthrop said. “This one’s going to hurt, but we’ve just got to worry about the next one.”

Mitch Leidner tallied two scores and 165 yards on 9-for-18 passing and had 84 yards and a touchdown on 13 rushes for the Gophers. Santoso missed an extra point pushed back by penalty in the second quarter, and his run up the middle on a fake attempt in the third quarter was stuffed at the goal line. But Kill said he never hesitated to send the redshirt freshman out for the long try. The Boilermakers, bracing for another fake, didn’t even rush to try for a block.

“I’m just thankful coach Kill has confidence in my ability,” Santoso said.

Gabe Holmes and DeAngelo Yancey caught passes for touchdowns, and Mostert put Purdue in front for the first time at 21-20 with a 42-yard burst. His 69-yard gain set up a touchdown run by Appleby that stretched the lead to 38-29 midway through the third quarter.

But the Gophers started to tackle better and put more pressure on Appleby, and Leidner did his part with deep passes to Donovahn Jones (42 yards) and Isaac Fruechte (45 yards) to set up a touchdown and a field goal. Then Leidner finished a drive kept alive by an overturned call of his fumble, finding K.J. Maye for a 37-yard completion that Maye punctuated with a somersault into the end zone to bring the Gophers within 38-36.

In the second quarter, Cobb lost a fumble that appeared to occur after his arm hit the ground, but officials disagreed. Then Appleby’s pass three plays later to Anthrop was ruled incomplete, though replays suggested a catch and a fumble. The call stood, and Purdue kicked a short field goal for a 24-20 lead.

Thompson’s interception on the first play from scrimmage set up a score by Cobb with 20 seconds elapsed on the clock, the fastest score by Minnesota in four seasons under Kill. Three plays later, Damien Wilson picked off Appleby for a 42-yard touchdown return wiped out by Theiren Cockran’s offside penalty. Then the Boilermakers shifted the tone of the entire game, with a 55-yard score off a bubble screen pass from Appleby to Anthrop.