Omaha's Quinton Urban drove in Tommy Clouthier with an RBI single in the top of the ninth to put Omaha in the lead for good Thursday night.
St. Joe's Jon Pomatto takes his first loss of the year allowing one earned run in his lone inning of work.
The late-inning collapse spoiled a solid outing pieced together by starter Jeremiah Figueroa and two relievers for the first eight frames.
Figueroa worked through 4 2/3 innings allowing just two earned runs despite surrendering four hits and four walks.
Grant Gavins and Austin Aspegren combine for 3 1/3 scoreless innings to bridge the gap into the ninth.
Despite digging a two-run hole, St. Joe fought back late in the game.
Ryan Abernathy scored on a Joe Koerper ground out in the sixth, and Francisco Alvarez brought Brandon Huske around with an RBI hit in the seventh to tie it at two.
That's all the offense could muster.
Abernathy and Mike Sherburne finished with two hits apiece, while Huske and Alvarez each finished with one hit. The rest of St. Joe's lineup went a combine 0-18.