Attorneys said the agreement was "amicable." Neither side agreed to be on camera when the agreement was reached. No terms of the deal were released.
The meeting between the two attorneys and a judge took place behind closed doors. Berry was not present, but Aubry was in court.
Aubry had been ordered to stay 100 yards away from Berry, Berry's current boyfriend actor Olivier Martinez, and Aubry's 4-year-old daughter with Berry, Nahla.
A temporary restraining order against Aubry was set to expire on Thursday. The restraining order stemmed from a fight between Martinez and Aubry that occurred on Thanksgiving.
Martinez and Aubry got into a fight outside Berry's home when Aubry was dropping off the couple's daughter Thursday. On Monday, graphic photos of the Canadian-born model emerged. Aubry claims Martinez threatened to kill him during the brawl that left him with a broken rib and a bruised face.
In the court documents, Aubry said he was about to get in his car to leave when Martinez told him they needed to talk.
"All of a sudden, Mr. Martinez jumped on me on the side of my body, and punched me such that he had taken me down to the ground. He continued to punch me at least two or three times, kicked me in the ribs with his knee or foot, and took my head in his hands and slammed it to the concrete driveway," Aubry claims in the documents.
The 37-year-old claims it all happened so fast that he didn't see Martinez coming and wasn't able to defend himself, as suggested by photos of Aubry's unmarked hands.
"While he was attacking me physically, Mr. Martinez said to me in an aggressive and threatening voice, 'You cost us 3 million dollars. When you see the judge, you're going to tell him you're going to Paris or I'm going to kill you. You're going to Paris, you're going to get your 20 grand a month in child support. From now on you're going to do drop offs on the street. I'm not just some [expletive] actor, you don't know me,'" Aubry said in the filing.
The latest claims were detailed in the court filings that prompted a judge to grant a civil restraining order against Martinez.
Aubry and Berry had been involved in a bitter custody battle over Nahla. A judge ruled last month that Berry could not relocate the child to France, where the Oscar winner was hoping to move with Martinez.
After the graphic photos of Aubry were made public, LAPD Cmdr. Andrew Smith said in a statement, "We always look into new information on cases we are investigating, but I think we have it right."