Kepler, 22, is having a breakout season, hitting .335/.410/.534 with three homers, eight triples, 22 doubles and 34 RBIs in 65 games. Kepler, who has seen time at first base and in the outfield, also has 12 stolen bases and 43 runs scored.
"I'm sure he's disappointed, like all of us are," said general manager Terry Ryan. "We would have certainly liked to have seen him in the game. But you have to be healthy enough to take the post, and he's not."
Kepler, a native of Germany, is Minnesota's No. 14 prospect, according to MLBPipeline.com. He was added to the 40-man roster during the offseason.
This is the second straight year the Twins have had a player scratched from the Futures Game due to injury, as Trevor May missed it in 2014 with a calf strain and was replaced by Alex Meyer. Triple-A Rochester right-hander Jose Berrios is now the organization's lone representative with Kepler unavailable.
• Reliever Ryan Pressly, who was placed on the 15-day disabled list with a strained right lat on Monday, is not expected to start throwing again for about four weeks. He's already started rehabbing his injury and is hoping to return in late August or early September.
• Outfielder Byron Buxton, who was placed on the 15-day DL with a strained left thumb on June 26, has a splint on his hand but has been working out at Target Field. He is able to participate in baserunning drills and can throw without any issues, but he's still weeks away from returning.
Rhett Bollinger is a reporter for MLB.com. Read his blog, Bollinger Beat, follow him on Twitter @RhettBollinger and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.