The National Weather Service issued the warning for southeastern Cook, northeastern Kankakee and central Will counties, which expired at 9:45 a.m.
The NWS said two to four inches of rain fell in the area, with up to another two inches of rain.
ABC7 Meteorologist Tracy Butler said the storms are expected to move out of the area in the morning hours, with some potential for spotty showers through the afternoon.
A Ground Stop was issued at both O'Hare and Midway airports due to the thunderstorms.