Before Tuesday's game against the Minnesota Twins, San Diego manager Andy Green said Capps saw doctors at a Minneapolis hospital after not feeling well Monday. After initially thinking it might be kidney stones, Capps found out it was a blood clot.
"A plan of action has not yet been determined for treatment, Green said.
Green also added that Capps will remain in Minnesota until he is cleared to fly.
"Stuff you hate to hear, really," Green said. "It's stuff I think they can manage long-term and put him in a good position with health in the future, but right now it just takes him out of competition for the rest of the year until that resolves."
The 27-year-old Capps missed the entire 2016 season after undergoing Tommy John surgery on his right elbow. He didn't pitch in the majors this year until Aug. 7.
Capps made 11 relief appearances with San Diego this season and had a 6.57 ERA.
The Padres acquired Capps in a trade with the Miami Marlins during the 2016 season, after Capps had his Tommy John surgery. He has a career 4.21 ERA in 129 relief appearances with the Seattle Mariners, Marlins and Padres.
Green was not certain how this latest setback will impact Capps for next season but he remained hopeful that Capps will be with the team in 2018.
"Really unfortunate for a guy who fought like crazy to get back from Tommy John," Green said. "He was just getting traction. In my mind, he was just starting to throw the ball really well. If you're going to bet on people, you bet on guys like him who work incredibly hard and are very resilient. You know he'll be back."
To replace Capps, the Padres purchased the contract of right-hander Cory Mazzoni from Triple-A El Paso. He appeared in eight games for the Padres earlier this season.