The National Weather Service issued the warning as a dangerous storm swept through several counties, including DeKalb, DuPage, Grundy, Kane, Kendall, Lake and Will.
Winds moving at 75 miles per hour raced through the area causing damage.
By 9:30 p.m., it appeared the storms were moving away from Chicago to the northeast.
Metra reported a "variety of delays and stops," mostly because of high winds. At 9:30 p.m., "more than 10 trains" were stopped on all Metra tracks, said Metra spokesman Michael Gillis, who described delays as "extensive."
An inbound train from Elgin to Chicago was stopped because of a tree that fell onto the tracks, Gillis said.
All Union Pacific Northwest Line trains and Union Pacific West Line trains were stopped, while some Union Pacific North Line trains were also affected, a Metra service advisory said.
At 9:30 p.m., 240,000 Commonwealth Edison customers were without power.
More than 300 flights were canceled at O'Hare Airport, while all fights in and out were delayed because of rain and thunderstorms both in the Chicago area and in other areas of the country, the city's Department of Aviation said.
A United jetliner at gate B-10 in Terminal One was picked up by a wind burst and blown 30 feet away from the building, according to a passenger. No injuries were reported, but passengers had to be quickly evacuated from jetways into safe areas.
Another passenger on a United flight scheduled to depart for Boston told ABC7 her plane was among dozens of fully-loaded jetliners stuck on O'Hare runways when the storm hit. The aircraft was rocked by high winds that made it sound as if the engines were revving and the plane was moving, she said. Many planes were unable to get back to gates because of widespread debris across airfield, according to the passenger.
At one point, thousands of people crowded into the underground tunnel connecting United's B and C concourses.
The Federal Aviation Administration confirms that during the peak of the storm the air traffic control tower was evacuated for about 15 minutes.
At Midway Airport, a number of flights were delayed up to two hours, while 30 were canceled, the department said.
The storms caused damage throughout Chicago and the suburbs and disrupted outdoor plans. Many residents reported downed trees and branches.
In Bolingbrook, tornado warnings sounded as winds ripped through the southwest suburb.
Conditions were so dangerous the Crosstown Classic was delayed at the U.S. Cellular Field.
There were no reports of serious injuries.
(Sun-Times Media Wire contributed to this report)