The Skyway was closed in both directions for two hours Wednesday night.
At first, investigators feared someone was randomly shooting at vehicles around 8:30 .m. Wednesday near 105th and Indianapolis Blvd.
The rocks damaged seven cars. Police arrested two boys, one 14 and the other 15.
Chicago police say they worked with Chicago Public Schools officials to developed information that implicated two CPS students.
The juveniles have each been charged with one count of felony vehicular endangerment and six counts of misdemeanor criminal damage to property.