Henderson went to the line with the score tied after an off-the-ball foul was called on Shaq Johnson as Ole Miss (17-2, 6-0 Southeastern Conference) was inbounding under its own basket. Frankie Sullivan's last-second heave for Auburn was off the mark, and the Rebels escaped.
LaDarius White led Ole Miss with 17 points and Jarvis Summers added 14.
Chris Denson had 18 points for Auburn (8-11, 2-4).
Ole Miss won it on free throws after a poor shooting night from the line overall. The Rebels were 2 of 15 before Henderson made two in the final seconds.
Auburn led 33-31 at halftime and by as many as nine before Ole Miss came charging back in the second half.
The Tigers jumped out to a 9-0 lead and were still up by nine after Noel Johnson's 3-pointer with 5:21 to play in the first half.
From there, Ole Miss went on an 11-4 run to cut the deficit to two at halftime. White scored on a layup a minute into the second half to tie the game.
Auburn trailed 61-56 with 3:30 to go before a quick 5-0 spurt tied the score with a minute to play. With less than 20 seconds left, Murphy Holloway blocked Denson's layup attempt and got the ball to the Rebels' Reginald Buckner in transition. But Shaq Johnson tracked down Buckner and blocked the ball out of bounds to set up the game's final sequence.
Shaq Johnson knocked Henderson to the floor as he rotated on the inbounds set and was whistled for a foul. Henderson hit both free throws to give Ole Miss a victory in a hostile environment.
Click here for more at Inside Ole Miss Sports Blog by Parrish Alford.
Read more in Sunday's NEMS Daily Journal newspaper.