Marmol was diagnosed with a strained right hamstring and will head back to Chicago for an MRI on Saturday.
"There is a chance we are going to have (to) DL him," Cubs manager Dale Sveum said.
On a night when the bullpen was strung out as far as possible, Marmol offered just two-thirds of an inning in a rocky outing that helped the Brewers regain the lead after a David DeJesus grand slam just a half-inning earlier.
No longer used in the closer role, Marmol entered in the seventh inning shortly after the Cubs had taken a 4-1 lead. Marmol got two relatively quick outs before a walk to Ryan Braun and an RBI double from Aramis Ramirez.
"(Marmol) was trying to say he was OK," Sveum said. "When he was pitching, you could tell in his face he wasn't right even though the ball was coming out of his hand OK. But he wasn't right."
He is almost guaranteed to go on the disabled list. Limping significantly after the game, Marmol said he wasn't sure whether a DL stint was going to happen.
But given the fact that the Cubs used every reliever in the bullpen and won't have Kerry Wood available, at the very least, they will need reinforcements. Wood, who has been used sparingly this season, pitched two innings Friday night, as did Rafael Dolis.
It is possible that Scott Maine could be recalled when Marmol is placed on the disabled list officially. Maine was pitching well for the Cubs before a roster numbers game had him on his way back to Triple-A Iowa. Maine was the only reliever at the time with minor league options and was sent down.
On a night Dolis blew the save by giving up two runs in the ninth inning, the relievers combined for nine walks. Dolis had two of those walks, while Wood contributed three. The Cubs gave up 14 walks total, one off the club record set in a 13-inning game in 1962.
In 15 games, Marmol is 0-1 with a 6.35 ERA.
ESPNChicago.com's Doug Padilla and The Associated Press contributed to this report.