Bryant was pulled from the game before the third inning and underwent X-rays on his left big toe on Saturday. The X-rays were inconclusive and precipitated the MRI.
There was no timetable for Bryant's return.
"He's been dealing with it for the last couple of nights and sucking it up because he's a freaking gamer," Iowa manager Marty Pevey told the Des Moines Register on Saturday.
Bryant, ranked No. 1 on MLB.com's list of top 20 Cubs prospects, is batting .306 at Triple-A. He leads all Minor Leaguers with 40 home runs combined at Double-A Tennessee and Iowa. His 40th homer was a walk-off blast in the 12th inning Thursday to give Iowa a 6-5 win over Las Vegas.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter @CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.