Desmonte Leonard turned himself in to U.S. Marshals at the federal courthouse in Montgomery, said Montgomery County Sheriff D.T. Marshall.
It was not clear when Leonard, 22, would be transported to Auburn.
The development came hours after a small army of law enforcement officers swarmed a Montgomery home where Leonard was believed to be hiding and came up empty-handed.
Police surrounded and searched the house for more than six hours, spraying “a powerful dose” of tear gas in hopes of flushing out the man accused of killing three people and wounding three others at nearby Auburn University.
They scaled down their efforts at the house Tuesday after they could not find Leonard, who was wanted on three counts of capital murder.
The officers from local, state and federal agencies looked frustrated, CNN affiliate WFSA reported.
Police defended the raid at a news conference Tuesday after reports surfaced that they had gone to the wrong house and used excessive force.
Montgomery Police Chief Kevin Murphy said he had every reason to believe Leonard had once been in the attic. Police called on him to come out. They did not get a response, although they heard coughing and detected movement in the attic.
By the time they launched a raid on the house, the suspect was gone.
“We didn’t go into that house foot by foot. We took it inch by inch,” Murphy said. “We didn’t want anybody else to get hurt. We did everything right.”
Police received three calls about Leonard being in the area; the third was from a woman who owned the house. She said she returned from work to find a man who looked like the suspect sitting on her couch, said Montgomery Mayor Tommy Strange.
She then ran out to her car and called police, he said.
Saturday night’s shootings took place at an off-campus apartment complex in Auburn, about 50 miles east of Montgomery. The dead included two former Auburn football players. A current football player was among the wounded.
“This has been an incredibly difficult 72 hours,” Gene Chizik, Auburn’s head football coach, told reporters Tuesday. “The whole Auburn family is devastated.”
“We’ve got a road ahead of us right now, and it’s a long road of grieving,” he said.
Police had posted a $30,000 reward for information on Leonard’s whereabouts.
Two other men have been jailed on charges of hindering prosecution in the case.
Auburn police said one of those arrested, Jeremy Thomas, 18, left the scene of the shootings with Leonard. Montgomery police say Gabriel Thomas, 41, tried to mislead investigators during the search, and they arrested him Sunday at the request of U.S. marshals.
Police did not immediately disclose the relationship, if any, between the two men. Both were arrested in Montgomery, but Jeremy Thomas was expected to be transferred to a jail in Lee County, which includes Auburn, police said.
Officers received a call reporting the shooting at the University Heights apartments clubhouse about 10:03 p.m. Saturday, Auburn Police Chief Tommy Dawson said Sunday.
Arriving officers found Edward Christian, 20, dead at the scene.
Christian, of Valdosta, Georgia, was off the football team because of an injury, Dawson said. Former player Ladarious Phillips, 20, and Auburn resident Demario Pitts, 20, died later at a hospital, he said.
Two others, including current Auburn sophomore offensive lineman Eric Mack, 20, of Cameron, South Carolina, were taken to East Alabama Medical Center in the nearby town of Opelika.
Mack was released from the medical center Sunday morning, while another man, Xavier Moss, 19, was treated and released from the same facility.
A third man, John Robertson, 20, was transferred to the University of Alabama at Birmingham Hospital, where he was in critical condition after being shot in the head.
Leonard and two other men were thought to have fled the scene in a white Chevrolet Caprice, authorities said. Police later found the car abandoned in an adjacent county, Dawson said.
Police have a motive in the shooting, but Dawson would not release it, saying “that’s for the courtroom, later on.” He did say authorities believe gunfire erupted during a fight at a party.
Several media outlets cited witnesses as saying the altercation was over a woman.
Witness Turquorius Vines told affiliate WGCL the violence was sudden.
“It went from us chilling with all these females to a massacre for no reason at all,” he said.
“I heard what appeared to be six or seven gunshots outside my apartment,” resident Nate Conoly told affiliate ABC 33/40. He said he couldn’t see anything when he peered outside his window, but heard screaming. “… I went back into my apartment and locked the door,” he said.
A woman identifying herself as only Leonard’s grandmother answered the telephone Sunday at an address listed as his in court records, the Montgomery Advertiser reported.
“I’m just very surprised by all of this,” she told the newspaper. “This is not the grandson I know, I can tell you that. I’ve just been sitting here, can’t hardly move, I’m so in shock by it. It just doesn’t seem real.”