The series loss is the first for Auburn in the SEC this season after the Tigers won their first three series in the conference.
The loss drops Auburn's record to 17-13 overall and 6-5 in the SEC. Alabama improves its record to 12-19 and 3-8 in conference play.
With the 1-0 count and two outs, Dugas hit a high fastball from reliever Slade Smith over the right field fence, scoring Hunter Gregory, who reached first base on a fielder's choice. Auburn almost converted a double play to end the game, but Gregory barely beat out Dan Glevenyak's throw to first.
"He pitched very well," said Auburn coach John Pawlowski of Smith. "Unfortunately, he left one ball up in the zone and good hitters do some damage with them. Unfortunately, that was the outcome of it.
"I thought we threw the ball well," added Pawlowski. "Unfortunately, you play 27 outs. That last out sometimes is difficult to get, and we couldn't get that last out today."
Despite giving up the game-winning home run, Smith pitched well in relief of starter Will Kendall, who was pulled from the game with two outs in the fifth inning with a strained elbow.
Smith gave up four hits, two walks and three runs in four innings. The loss brings Smith's record to 2-4 on the season. Alabama's Trey Pilkington (1-0) picked up his first win of the season for the Tide.
Kendall was solid once again for the Tigers, giving up five hits and zero earned runs in four and two/thirds innings. Pawlowski said Kendall will see a doctor on Monday for an evaluation.
"We've got to come back and regroup tomorrow," said Pawlowski. "Obviously, a disappointing loss. Every loss is disappointing, but our guys know what the challenge is, so they'll come back tomorrow and be ready to go."
Auburn scored two runs in the sixth, giving the Tigers a 3-2 lead. Creede Simpson walked to start the inning and advanced to second on a single by Ryan Tella. Garret Cooper squared and hit a sacrifice bunt and reached base on a throwing error, which also allowed Simpson to score the go-ahead run and Tella to advance to third.
Ryan Tella slides under the tag of Brett Booth to score.
The Tide fought back in the bottom of the seventh. With two outs, Gregory singled up the middle to bring home Jon Kelton, who walked to start the inning, bringing the Tide within one run at 3-2.
Auburn got on the board first in the third inning when Caleb Brown doubled in Zach Alvord, who had singled to right. Glevenyak then singled putting runners at the corners with no outs. But the Tigers couldn't capitalize, with Gonzalez lining out to second and a Simpson grounder to third leading to Bowen being thrown out at home.
In all the Tigers left seven runners on base on the evening and committed two fielding errors.
Tella again led the way for the Tigers at the plate, going 2-for-4 with one run scored. Auburn had only six hits on the afternoon after getting 16 Friday against the Tide.
Auburn and Alabama will meet at 1 p.m. Sunday for the third and final game of the series.