In 15 starts this season, Bauer had never thrown fewer than five innings.
"We had to do that to keep him in consideration, that was the plan," D-backs manager Kirk Gibson said. "We'll make that decision, you guys can speculate, we don't have to do anything until Thursday."
The D-backs need a starter to pitch the finale of their series with the Braves after Joe Saunders went on the disabled list on Saturday with shoulder inflammation.
Bauer struck out five in Salt Lake City on Sunday, allowing two hits, two walks and a run in his short outing.
"Figured just to cut him short, that way he could have a nice little tune-up if we decide he's the guy," D-backs Executive Vice President & General Manager Kevin Towers said on the television broadcast of Sunday's game. "I'll let you guys do all the speculating, but I think we have a pretty good idea of what we're going to do."
The club has a day off on Monday, giving it the opportunity to skip the fifth spot in the rotation, but Gibson said before Sunday's game he doesn't want to go that route.
"I don't think so, no," Gibson said when asked of the possibility of skipping the spot. "All along I want to leave them in turn. We have a streak of 13 games before the All-Star break and a streak of 20 games after the All-Star break, so I don't think this would be a smart time to move guys up if you have the ability to give them an extra day."
The D-backs selected Bauer with the No. 3 overall pick in last year's First-Year Player Draft, and he was ranked the No. 1 D-backs prospect -- and sixth-best prospect in baseball -- by MLB.com this spring.
Through 93 1/3 innings in 2012, the right-hander has struck out 116 batters. He boasted a 1.68 ERA in eight starts with Double-A Mobile, and has a 2.82 ERA in eight starts in Triple-A.
Tyler Emerick is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.