Director Michael Bay says the city has been gracious with requests to blow up Michigan Avenue and base-jump over the Chicago River.
Crews in the area were set to finish up filming on Thursday, but shots scheduled for that day were put on hold after a bank teller working as an extra was critically injured while shooting a scene in Hammond, Ind., on Wednesday.
"The filming that was canceled was not rescheduled," Moskal said.
The Indiana Department of Labor is investigating the accident.
When the shooting schedule for the film was announced earlier this summer, officials said they expected the movie to bring more than 200 jobs to the city.
Mayor Richard Daley also touted the city being used as a backdrop as "free publicity."
"You'd be surprised how many people say they saw us in a movie," he said in June.
Chicago offered no financial incentives to the movie's producers, but the State of Illinois does offer a 30 percent tax credit for films made in the state.
"Transformers 3" is slated for release next summer.