The Gators snapped a 5-5 tie with a run off losing pitcher Brain Reed (1-1) in the eighth inning to hand the Crimson Tide its first back-to-back losses of the season.
Designated hitter Stephen Barton drew a one out walk and then stole second base with two outs to set up the winning run.
Dowdy, hitless in his four previous at-bats, stroked a two strike, two-out, two strike single to score Barton with the go-ahead run and give the Gators a 6-5 lead. Dowdy's RBI single was the first run allowed by the Alabama bullpen in 22 2/3 innings over the last six games.
In a gutty performance out of the pen, Reed allowed only one run and four hits in a career high 5 2/3 innings on the mound. He walked two batters and added six strikeouts in the loss.
Florida right-hander Darren Day (2-1), the last of five Gators pitchers used by Pat McMahon, picked up the win with two scoreless innings of relief. He allowed only one hit and fanned two batters, including Adam Pavkovich on a called third strike to end the game.
Alabama (18-5, 4-2 SEC) has lost back-to-back games for the first time this season and has now lost three straight SEC road series, dating back to last year.
The see-saw game began in the very first inning as it only took Alabama two batters to equal Saturday's run production as second baseman Allen Rice drilled a 3-2 fastball over the wall in right field to stake the Crimson Tide to an early 1-0 lead. It was Rice's fifth home run of the season and third in SEC play.
Florida (19-6-1, 2-3-1 SEC) quickly tied the game in the bottom of the first inning with three base hits of Allen Ponder. Jonathan Tucker reached on a one out single to center and moved into scoring position on a balk. C.J. Smith followed with a two-strike single to field. Ben Harrison followed with a single to left, but Ponder avoided further damage.
The first inning continues to be trouble for Alabama since entering league play. In six SEC games, Alabama has been outscored 12-3 compared to a20-1 scoring advantage in 17 non-conference games.
Florida took its first lead of the game in the second inning when Brian Rose reached on hit to left field that was misplayed into the double by Brandon Avalos. Stephen Barton moved Rose to third with a sacrifice bunt and Justin Tordi's slow rolling ground ball to third chased Rose home with the 2-1 UF lead.
Alabama took its first lead of the game with three runs in the third inning to chase starter Christian Madson.
Nathan Meiners, making his first career SEC start at third base in place of Evan Bush, doubled over the head of Harrison in center field to open the inning. After Avalos popped up on a bunt attempt, Travis Garner singled through the left side of the infield, scoring Meiners with the tying run.
Garner's base hit chased Madson, who allowed three runs and four hits in 2 1/3 innings for the Gators.
Rice greeted left-handed reliever Tom Potter with a a sharp single up the middle and Adam Pavkovich dumped a double over the head of Smith at first base, scoring Garner and moving Rice to third base.
Beau Hearod followed with sacrifice fly to right field to score Rice and put the Crimson Tide in front 4-2.
Florida got the three runs back and re-took the lead in the bottom of the inning on a pair of walk to Tucker and Smith and three-run home run right-center by Mario Garza. It was Garza's sixth home run of the season. It was also the first home of the series for the Gators, who led the SEC with 33 home runs.
Ponder left the game in the third inning after allowing a single to Jeff Corsaletti. Ponder slipped on the mound during his follow through and hyper-extended his knee. The freshman right-hander got a good report from the training room and should be fine.
Ponder, who struggled with his breaking ball, allowed five runs and six hits in 2 1/3 innings before leaving with the injury. He walked two batters and did not record a strikeout in his first career start for the Crimson Tide.
Alabama wasted a golden opportunity in the fifth loading the bases with one out, but failed to score a run against reliever Bryan Ball.
Avalos opened the inning with a single to left field and was erased at second base when Garner tapped into a force play. Rice was then hit by a pitch and Ball replaced Potter with two on and one out.
Ball then walked Pavkovich to load the bases, before getting Hearod on a pop up to short and Welch to ground out to second to end the inning.
The fifth inning eventually proved fatal for Alabama, which lost its third one-run game of the season.
After leaving the bases loaded in the fifth, Alabama made the most of its two hits in the sixth to tie the game. Charlie Lyons and Meiners slapped back-to-back singles to left field with one out. Lyons took third on the hit by Meiners, who moved up one base on a fielding error by Garza in left.
Avalos then flied out to center field, chasing Lyons home with the tying run. The UF third baseman saved another run, making a diving stab of a sharp ground ball by Garner and firing over to first base to end the inning.
Florida threatened with a two-out rally in the seventh inning as Garza drew a two-out walk and Harrison singled up the middle sending pinch-runner Jake Riordan to third base. Reed then got Jeff Corsaletti to ground out to end the inning and keep the game tied at 5-5.
The Gators finally pushed the winning run across the plate in the eight for the one-run win.
Alabama wraps up its five-game road trip on Wednesday night with a 7 p.m. game against UAB at Young Memorial Field in Birmingham. The Crimson Tide returns home nest weekend as they host the LSU Tigers in a three-game series beginning Friday, March 28 at 6:30 p.m. The Gators host Tennessee next weekend in a three-game series here in Gainesville.