Zambrano had thrown 34 pitches. After a pitch to Eli Whiteside, Zambrano walked off the mound and catcher Koyie Hill and trainer Mark O'Neal came to the mound. Zambrano then went to the dugout and was replaced by Marcos Mateo. After leaving the game, Zambrano went to Northwestern Memorial Hospital to get an MRI.
The Giants were leading 1-0 at the time on an unearned run aided by a Zambrano error.
The Cubs went on to win 5-2 in 13 innings, with pinch hitter Geovany Soto's three-run homer capping a four-run rally.
Zambrano has struggled at times this season but had been pitching well of late, going at least seven innings in his previous two starts against the White Sox and Kansas City.
Zambrano suffered from lower back spasms in 2009 that landed him on the DL for over three weeks.
The Cubs could ill afford another injury to a starting pitcher. Andrew Cashner, Randy Wells and Matt Garza have all spent time on the DL. Cashner remains sidelined and may start playing catch next week. Kerry Wood is scheduled to come off the DL on Friday after suffering from a blister on his right index finger.
ESPNChicago.com's Bruce Levine and The Associated Press contributed to this report.