Bochy said Pagan underwent an MRI that revealed inflammation, adding that he wanted to see the leadoff hitter's ailment "calm down" before he would rejoin the lineup.
Pagan also missed starts June 8-9 with a leg ailment. He entered Tuesday batting a team-best .307 with 11 stolen bases in 14 attempts.
Chris Haft is a reporter for MLB.com. Read his blog, Haft-Baked Ideas, and follow him on Twitter at @sfgiantsbeat. This story was not subject to the approval of Major League Baseball or its clubs.