Juan Perez replaced Pagan to make his 16th start of the season.
Manager Bruce Bochy expressed hope that rest and treatment would allow Pagan to return to the lineup Tuesday, but Pagan wasn't as optimistic.
"Do I feel better after treatment? No," Pagan said after the Giants' 6-2 loss Monday night. "It's tough to say tonight, but let's see how I feel tomorrow. Tomorrow I hope to have a better answer for you."
Back inflammation put Pagan on the disabled list for 44 games from June 15-Aug. 6. Since his reinstatement, San Francisco's switch-hitting leadoff hitter had appeared in 30 of 32 games, batting .295. He's hitting .302 overall.
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.