Michael Ward, 18, and Kenneth Williams, 20, both of Chicago, were charged with first-degree murder, attempted murder and aggravated battery with a firearm.
Police said Ward confessed and was believed to be the shooter, the Chicago Tribune reported.
Police Superintendent Garry McCarthy said at a news conference Williams, who had been shot in July, and Ward targeted the group Hadiya was with because they wrongly believed they were members of the gang responsible for wounding Williams.
Hadiya's father, Nathaniel Pendleton, said news of the arrests had brought a "legitimate" smile to his face for the first time since his 15-year-old daughter was killed in the Jan. 29 park shooting that left two other teenagers wounded.
"I'm ecstatic that they found the two guys," he told the Tribune in a telephone interview from a restaurant in Washington where he was with his wife, Cleopatra Cowley-Pendleton, and other relatives. "[I'm] thanking God that these two guys are off the streets, so that this doesn't happen to another innocent person."
The Pendleton family was in the nation's capital to be guests of President Barack Obama while he delivers the State Of The Union address Tuesday night, the newspaper said.
First lady Michelle Obama attended Hadiya's funeral Saturday in Chicago.