A Department of Construction and Permits spokeswoman says the team paid a penalty of $6,725 for lacking permits for $2 million in repair work.
Sabrina Miller says the Cubs also paid $36,010 for two permits issued retroactively for the work.
Team officials have said they weren't aware permits were required. It was a claim derided by Mayor Richard Daley.
Safety has been an issue at Wrigley since three small chunks of concrete fell from the upper deck. That led to the city's discovery that the repair work had been done without city permits.