With the loss, Baylor (34-23) falls into the loser's bracket and will take on the loser of Friday night's game between Lamar and TCU in an elimination game at 2 p.m. Saturday.
Arizona (34-22) trailed twice in the game, but both times the Wildcats answered with crooked numbers to take the lead in their next at-bat.
The Bears took a 1-0 lead in the third when Gregg Glime knocked his eighth home run of the season for the first hit of the game against Wildcat starting pitcher Kurt Heyer, but Heyer worked his way out of a bases-loaded, one-out jam to limit the damage.
That proved crucial, as Arizona quickly tied the game with Steve Selsky's home run that curved just inside the foul pole down the right-field line, and after a hit batter, Josh Garcia gave the Wildcats the lead with a two-run shot of his own.
Logan Verrett walked the next batter, and after a flyout for the first out of the fourth, Shawn Tolleson was summoned from the bullpen. Tolleson got out of the inning, held Arizona scoreless in the fifth, and the Bears rallied for three runs in the bottom half of the frame.
Brooks Pinckard reached on a leadoff double, and Cal Towey brought him around to score with a one-out double to cut Arizona's lead to 3-2. Joey Hainsfurther's grounder to third would've been the second out, but Seth Mejias-Brean fell down trying to throw to third, putting runners on the corners with one out.
Max Muncy followed with a sacrifice fly to tie the game at 3-3, and Glime again gave the Bears the lead when he drilled a RBI double to the wall in right field, but Arizona quickly regained the lead with five runs on only two hits in the sixth.
The Wildcats singled twice to bring around an insurance run in the seventh for a 9-4 lead, but the Bears threatened when they loaded the bases with none out in the bottom half of the inning.
However, Arizona escaped the jam unscathed with a strikeout, a popout and a groundout. The seventh inning was the third time in the game that Baylor didn't score after loading the bases with less than two outs; the Bears had the bases loaded with one out in the third and fourth innings.
The Bears nearly came back to tie the game after plating five runs in the bottom of the ninth, but Logan Vick was left standing on third base as the potential tying run when Raynor Campbell lined out to right to end the game. Pinckard had a two-run single, Muncy singled in a run and Glime collected another RBI with a run-scoring groundout.
Tolleson (2-7) took the loss after allowing six runs - one of which was earned - on five hits in 3.2 innings. Heyer (7-4) earned the win by holding the Bears to four runs on six hits with four walks and five strikeouts in 6.0 innings.
Glime finished 2-for-4 with a walk, a double, a home run and three RBI, while Towey and Pinckard each had two hits for the Bears. Alex Mejia led the Wildcats at the plate, going 3-for-4 with four RBI, while Joey Rickard and Rafael Valenzuela each went 2-for-5 with one RBI.
Baylor looks to rebound in a 2 p.m. elimination game on Saturday against the loser of Friday's second game between TCU and Lamar. Should the Bears win on Saturday, they'll play again at 2 p.m. Sunday. With a win on Sunday afternoon, Baylor would qualify for the Championship Round, where they would need to win at 7 p.m. Sunday and again at 7 p.m. Monday to win the Fort Worth Regional.