Pavkovich's two-out single to left drove home the winning run from second base as Brown beat the throw to the plate from left fielder Jeff Cook.
Alabama (24-5) trailed 3-0 entering the seventh inning and scored two runs in each of its last two at-bats to win its 10th straight game over Southern Miss, the second-longest active winning streak by Alabama over any opponent.
"We are glad to get the win," Alabama head coach Jim Wells said. "To their credit, (Stewart) pitched very well, and to our credit we battled back and won the game. Pavkovich had two big hits for us tonight." The winning rally started with back-to-back walks to Peter Stonard and Jeremy Brown by losing pitcher Brian Hurley (2-1).
Stonard and Brown drew back-to-back walks to open the inning and after Hearod fouled off a bunt attempt with two strikes for a strikeout, Boyd was hit by a pitch to load the bases. Rice followed with a sacrifice fly to center, scoring Stonard with the tying run.
Pavkovich, a native of Venice, Fla., collected two hits and two RBI to lead the Crimson Tide to its 22nd consecutive home win. Since March 12, Pavkovich is batting .350 (16-for-40) with two home runs and nine RBI. The win over Southern Miss was his third game-winning RBI of the season and fourth multiple hit game of the season.
Alabama scored two runs in the seventh inning to break its 6 1/3 inning scoring drought, cutting the USM lead to 3-2. The Crimson Tide also stranded the bases loaded when Garner flied out to right field to end the inning.
Hearod put the Crimson Tide on the board in the seventh inning as he drilled a solo home run to left-center field to cut the Golden Eagles lead to 3-1. It was Hearod's seventh home run of the year third in his last four games.
Boyd followed with a double to center field and scored an Pavkovich's two-out double into the left field corner, cutting the deficit to 3-2.
USM starter Daniel Stewart was replaced by closer Brian Hurley, who gave up and infield single to Grant Redding and walked McClanahan to load the bases. Hurley got out of the jam when Garner flied to right to end the inning, leaving three men on base.
Stewart worked 6 2/3 innings and allowed two earned runs and six hits in his best outing of the season. He entered the game having allowed 50 hits in 34 innings of work and sported a 5.82 ERA. Stewart walked two and added four strikeouts.
Southern Mississippi (18-11) broke a scoreless tie in the top of the fifth inning with three consecutive two out hits to take a 2-0 lead. Allen Winningham started the rally with a single through the right side of the infield. Left fielder Jeff Cook followed with a double to left field, putting runners on the corners. Brad Willcutt dribbled an 0-2 pitch inside the third base bag for a two-run double, scoring Winningham and Cook to give USM a 2-0 lead.
The Golden Eagles added an unearned run on the sixth inning to take a 3-0 lead over Alabama. Jarrett Hoffpauir reached on a three-base error when right fielder Chad White over ran a pop fly down the right field line.
Brian Reed came on to relieve starter Jeffrey Norris and gave up an RBI single to left to Jason Lowery as USM extended its lead to 3-0. The Golden Eagles put two more men on base in the inning but did not score. Lowery was picked off at second base with no outs and then Reed worked out of the jam.
Norris, making his second of the year, pitched five-plus innings and allowed three runs on six hits. He did not walk and a batter and struck out two. He was charged with only two earned runs.
Reed (2-0) pitched a career high four innings and scattered five hits for his second career win. The junior also hit one batter and struck out two, including Willcutt on a 0-2 pitch to end the game, stranding the tying run at third base.
USM outhit Alabama 11-8, but stranded 10 base runners, including at least one base runner in seven of the nine innings.
Alabama threatened only twice in the first six innings of Daniel Stewart, but did not score. Peter Stonard reached on a one-out double in the fourth inning and was stranded at third base as Jeremy Brown struck out and Beau Hearod grounded out to end the inning.
The Crimson Tide put the first two runners on base in the sixth inning as Chad White walked and Scott McClanahan singled to center. Travis Garner lined into a double play on a sacrifice bunt attempt, doubling up White at second base. Stonard grounded out to end the inning.
Cook led Southern Miss with three hits, including a double and one run scored. Willcutt, Hoffpauir and Lowery also doubled for the Golden Eagles.
In addition to Pavkovich, Boyd was the only other UA player with more than one hit, collecting a single and double.
Alabama will host Austin Peay on Wednesday night at 6:30 p.m. at Sewell-Thomas Stadium. Southern Miss travels to Charlotte for a three-game series beginning this Friday.