There was speculation something was wrong with Kimbrel when Farrell went to Koji Uehara for the save following a team off-day on Thursday.
Setup man Junichi Tazawa was also unavailable on Friday with right shoulder discomfort. The Red Sox should have more information by Saturday on how much time Kimbrel will miss.
"He was unavailable," Farrell said. "After pregame conditioning and BP he came in complaining of some left knee discomfort. He was sent for an MRI here tonight. We'll get a better read once those images are viewed. So we won't have a further update until tomorrow."
Kimbrel was one of six Red Sox players selected for the 2016 All-Star Game presented by MasterCard.
In 34 appearances this season, Kimbrel has 17 saves and a 3.55 ERA.
The Red Sox weren't aware of Kimbrel having a knee issue until late Friday afternoon.
"Everything that we did early, he was fine," Farrell said. "But then he felt something while the running was taking place unfortunately during BP while he was shagging."
Without two of their key relievers, the Red Sox still held on for a tight win, as Robbie Ross Jr., Heath Hembree, Matt Barnes (three strikeouts in the eighth) and Uehara recorded the final 12 outs.
Coverage for the All-Star Game will begin Tuesday at 7:30 p.m. ET on FOX.
Ian Browne has covered the Red Sox for MLB.com since 2002. Follow him on Twitter @IanMBrowne and Facebook. This story was not subject to the approval of Major League Baseball or its clubs.