Scratching the switch-hitting Pagan, who has a history of back problems, threatened to hamper San Francisco's already challenged offense. He hit .333 (2-for-6) in the series' first two games and owned a .455 career batting average (5-for-11) off Cubs starter Jake Arrieta.
Pagan, who's eligible for free agency after this season, appeared in 129 regular-season games and batted .277 with 12 home runs, 55 RBIs and a team-high 15 steals in 19 tries.
Pagan joined third baseman Eduardo Nunez on the list of Giants regulars who are enduring injuries.
Chris Haft has covered the Giants since 2005, and for MLB.com since 2007. Follow him on Twitter at @sfgiantsbeat and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.