The Commodores (6-4, 3-3 Southeastern Conference) are now bowl eligible for the second straight season for the first time in school history.
Vanderbilt trailed 23-6 early in the third quarter, but Rodgers found Jordan Matthews for a 52-yard touchdown minutes later to start the Commodores' rally.
Rodgers completed 20-of-35 passes for 267 yards and two touchdowns. Matthews caught nine passes for 153 yards and a touchdown.
Ole Miss (5-5, 2-4) must beat either LSU or Mississippi State over the final two weeks to become bowl eligible for the first time since 2009.
Vanderbilt has won six out of eight games against Ole Miss.
Ole Miss wasted a terrific performance from Bo Wallace, who completed 31 of 49 passes for 403 yards and a touchdown. It's only the fifth time in school history a quarterback has thrown for more than 400 yards. Ja-Mes Logan caught eight passes for 160 yards.
The Rebels looked like they might hang on for the win after Bryson Rose kicked a 27-yard field goal to push them ahead 26-20 with 2:43 remaining.
But Vanderbilt drove the field in less than two minutes on nine plays, showing a moxie rarely seen from the Commodores before the arrival of coach James Franklin two years ago.
Boyd was wide open down the sideline on the game-winning play, catching Rodgers' perfectly-thrown ball and jogging into the end zone untouched.
It was a stunning conclusion considering nothing went right for Vanderbilt early in the game.
Zac Stacy -- who is the school's all-time leading rusher and came into the game with 752 rushing yards and six touchdowns this season -- was injured on his second carry and had to be helped off the field.
He didn't return and the Commodores' offense struggled to find any early rhythm without him.
Ole Miss scored first on a 9-yard pass from Wallace to Vincent Sanders, before Vanderbilt started a parade of field goals with a 22-yarder to pull within 7-3.
The Rebels moved the ball well in the second quarter, but had to settle for three field goals from Rose. The senior hit them from 22, 28 and 41 yards to push the Rebels' lead to 16-3 by late in the second quarter.
Casey Spear hit a 44-yard field goal just before halftime to pull Vanderbilt within 16-6 at halftime.
Ole Miss jumped ahead 23-6 early in the third quarter on a 1-yard touchdown run by Wallace. The short touchdown run was set up by several accurate throws from Wallace, including a 13-yarder to Scott that put the ball at Vanderbilt's 1.
Wallace's performance this season has mirrored the team's this season -- occasionally spectacular but equally mistake-prone. He came into the game tied for the league lead with 10 interceptions, but avoided the costly mistakes against the Commodores.
Instead, it was the Ole Miss defense that was having problems in the second half. Rodgers hit Matthews in stride for the 52-yard touchdown pass and then the Commodores finished an 11-play drive with a 1-yard touchdown run by Wesley Tate to pull within 23-20 with 2:33 remaining in the third quarter.
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