Shortstop Brodie Greene capped a big offensive day with a two-run homer off Baylor reliever Brooks Pinckard with two outs in the bottom of the 10th.
The Aggies (40-19-1) won the conference's automatic bid to the NCAA tournament. The Bears (34-22) will find out Monday if they're in. Texas and Oklahoma are already guaranteed berths after they were selected Sunday to host regionals.
Baylor led 3-0 after seven innings, behind starting pitcher Willie Kempf. But the Aggies got two runs in the eighth and another in the ninth to force extra innings.
Green, who finished the game 4-for-5 with two RBIs and two runs, was named the tournament's most valuable player.
It was Texas A&M's second Big 12 championship, adding to its 2007 title. Baylor fell to 0-6 in Big 12 title games.
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