Darkins set a school record with 294 yards, getting 231 and all three of his touchdowns in the second half of Minnesota's 39-38 victory.
But in a virtual replay of the teams' last two high-scoring games, the Golden Gophers, 3-1 overall and 1-0 in the Big Ten, still needed Cory Sauter's one-yard sneak and his two-point conversion pass to Ryan Thelwell with 1:38 left for the decisive points.
Purdue (2-2-1, 0-1-1) then got a 45-yard kickoff return from Lee Johnson, but Brad Bobich missed a 42-yard field goal attempt with 21 seconds to play, giving Minnesota a victory critical to its hopes of playing in a bowl game for the first time in nine years.
It was the fourth time in five games Purdue had the game decided in the final seconds, and it was the second time Bobich had failed to deliver a victory. He missed a 47-yard field goal as time expired in Purdue's 35-35 tie with Michigan State two weeks ago.
Darkins, who broke the school rushing record of 282 yards set in 1924 by Clarence Schutte, scored on runs of seven, 24 and 45 yards. He had rushed for 234 yards in a 49-37 loss at Purdue last season.
Purdue fullback Mike Alstott, who set a school record last week with his fourth consecutive 100-yard game, had 100 yards and two touchdowns.