The crash occurred just before 1:10 a.m. on the southbound Dan Ryan at 67th Street, Illinois State Police said. One person was injured.
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A car appeared to be completely engulfed in flames on the side of the expressway, causing Red Line trains to stop near 69th Street in Chicago's South Side Grand Crossing neighborhood.
Trains began running again just after 1:30 a.m., according to a tweet from the CTA.
Police said the crash involved only one vehicle, which had hit a concrete barrier.
A separate incident a few hours later caused Red Line service to be temporarily suspended between Garfield and 95th Street, due to debris on the tracks.
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State police responded to the southbound Dan Ryan near 75th Street about 2:40 a.m. for a four-vehicle crash, which resulted in another car fire and debris on the train tracks.
Three people were transported to a local hospital with non-life threatening injuries after the second crash, police said.
All southbound lanes were closed at about 3 a.m. They reopened just before 4 a.m.