The Ole Miss senior point guard had 25 points, including two free throws for the lead with 2 minutes, 56 seconds left, as the Rebels rallied from an 11-point second-half deficit to win 68-63.
Playing before an announced attendance of 7,903 paid fans at Tad Smith Coliseum, the Rebels also got a double-double from senior guard Zach Graham with 17 points and 10 rebounds.
While Warren took over in the second half, Terrance Henry and Graham each hit two free throws in the final 30 seconds to seal the win.
Ole Miss lost road games at Mississippi State and South Carolina over the last week, likely taking itself out of contention for an NCAA tournament at-large bid, but Rebels coach Andy Kennedy thought his team played with great effort.
"As a coach you're thinking of a million things, but you only want your players to think of one thing ... play hard," Kennedy said. "Down 11 with 13 and change left we challenged them to play hard. I thought our effort was tremendous."
Ole Miss (18-11, 6-8 SEC) needs wins at Auburn on Wednesday and at home against Arkansas next Saturday to finish with a break-even season in conference play. Alabama (19-9, 11-3) had already clinched the SEC Western Division top seed coming in and had won 14 of its last 16 games.
The Crimson Tide held Warren to 2-for-10 shooting and without a field goal until less than 2 minutes remained in its 74-64 win in Tuscaloosa on Feb. 12.
The harassment continued in the first half when Warren was 0 for 4 from 3-point range, but he got his teammates involved with four assists during that time. He finished 7 for 16 from the floor, 2 for 8 from the arc. Coming off a career-high 33 at South Carolina, Warren has 58 points in his last two games.
"I came out more aggressive. At Alabama, I didn't come out with enough aggression for my team. We all came out aggressive from the beginning as opposed to coming out flat."
The Rebels held a 35-30 halftime lead, but Alabama opened with a 21-5 run in the second half to lead 51-40 on Chris Hines' three-point play with 13:34 left.
Ole Miss responded with a 16-5 run getting nine points from Warren, who capped it with an assist to Nick Williams to make it 56-56 with 4:44 remaining.
The Rebels were 27 for 34 from the free throw line, and that was the difference in the game, Alabama coach Anthony Grant said.
Grant had a hand in those free throws when he was called for a technical foul with 2:42 left, arguing a call that went against Alabama's Senario Hillman. Warren hit one free throw off the technical and Graham two more off the foul to make it 61-58.
"You never want to give away free points," Grant said. "I disagreed with the call, and I let him know my opinion."
Henry's free throws made it a 66-63 game with 29 seconds to play. After a timeout with 17.4 seconds left, Alabama point guard Trevor Releford drove into the lane and turned it over. Graham was fouled in the aftermath and knocked down two to make it 68-63.
Kennedy played primarily zone defense in the second half to try and contain Crimson Tide forward JaMychal Green, who finished with a team-high 17 points, including a three-point play with 36.9 seconds left to make it a one-point game and keep the pressure on.
"We didn't start the second half ideally, but we played with a sense of urgency," Kennedy said. "Chris was more aggressive off the bounce, and we were gritty. It was a big win for our guys. We certainly needed it."