McInnis (3-0), who was an all-state performer at Rankin High School, took a no-hitter into the eighth inning in his third collegiate start for Southern Miss.
UA senior center fielder Emeel Salem broke up the no-hit bid with a two-out infield single in the top of the eighth inning as the Crimson Tide avoided being no-hit for just the third time in the program's 115-year history and the first time since 1967.
McInnis, who threw 124 pitches, left the game after Jeff Texada popped up to first base to end the eighth inning. He added six strikeout and four walks in the game.
"McInnis was really good," Alabama head coach Jim Wells said. "He gave us a lot of fastballs and we had some opportunities to hit. But, give him all the credit, he did a really good job. Certainly, you don't go eight innings with only one hit. That was really disappointing."
Left-hander Tyler Conn pitched the ninth inning to preserve the shutout, but allowed a two-out single to Ryan Rhoden as the UA finished with two hits.
Alabama (12-3) saw its six-game winning streak end with the loss to Southern Miss.
It was only the third shutout in series history by the Golden Eagles and first since 1977.
USM left fielder James Ewing did all the damage on offense for the Golden Eagles with a 2-for-4, three RBI night at the plate. He drove in the first run with an infield single in the first inning and then broke the game open with a two-run single in the fifth as the Eagles took a four-run lead.
Southern Miss (11-2) took advantage of a pair of walks against Alabama starter Bernard Robert to take a 1-0 lead in the first inning. Trey Sutton and James Ewing drew back-to-back walks with one out. After Luke Adkins reached on a fielder's choice, Ewing rolled an infield single to short to score Sutton with the first run of the game.
The Golden Eagles plated an unearned run in the bottom of the fourth inning to double its lead to 2-0. Bailey Hartel stroked a one-out double to right center and moved to third on Jody Blount's infield single. Hartel scored on the play when shortstop Greg Paiml's throw got past first baseman Matt Bentley to allow both runners to advance.
Southern Miss doubled its lead again in the fifth inning when Michael Ewing bounced a two-out single up the middle to score two more runs and give the Golden Eagles a 4-0 lead.
Brian Dozier led off the inning with a double into the left field corner and moved to third on Sutton's bunt single up the first base line. After James Ewing grounded out and Adkins flied out, Robert was one out away from escaping without any damage before Ewing's two-run single chased him from the mound.
Sutton, Dozier and Blount also had two hits each for the Golden Eagles.
Robert (2-1) worked 4 2/3 innings and allowed four runs (three earned) and six hits. He walked three and fanned two in his second start of the season.
USM made it a 5-0 game in the eighth inning off reliever Will Stroup, who gave up a two-out single to Sutton.
Alabama returns home Wednesday night for a 6:30 p.m. (CST) game with Tennessee Tech. The game will be aired on the Crimson Tide Sports Network beginning at 6:20 p.m. The game will also be televised locally by WVUA Sports.
*The Alabama-Southern Miss game was played at Trustmark Park in Pearl, Miss., the home of the Southern League's Mississippi Braves. The park opened in 2005 when the Atlanta Braves Class AA affiliate moved from Greeneville, S.C. to Pearl.
*The Southern Miss game marks the first of five games this week for the Crimson Tide baseball team. Alabama returns home on Wednesday, March 7 to face Tennessee Tech before hosting No. 17 Nebraska this weekend in a three-game series.
*In addition, the Southern Miss game is the first of seven games in the state of Mississippi for the Crimson Tide baseball team this season. Alabama will also play at Ole Miss (March 23-25) and at Mississippi State (May 17-19) later this season.