Brown and Houston exchanged smiles during a 5-minute court hearing where Judge Barry Zimmerman ruled there was enough evidence to continue with the case against Brown.
The singer was ordered to turn himself in to authorities July 10 or 11 for fingerprinting when he would be released on a $2,000 bond. The judge also warned Brown against having "violent contact" with Houston.
The couple left the courtroom walking arm-in-arm and made no comment to reporters and television cameras waiting outside.
Brown's attorney Maurice Bennett said the judge's decision was expected.
Simple battery is punishable by up to a year in jail and a $1,000 fine. Normally on a first offense in domestic-violence cases, the charge is dismissed if the defendant undergoes counseling.
No date was set for when the case will be heard in state court. "It could be as much as a year down the road," said Lanny Lipsky, senior court clerk.
Houston called police Dec. 7 to report that Brown threatened to beat her "and then struck the left side of her face with an open right hand," a Fulton County police report said.
Brown addressed the report's specifics in an April interview with Dateline NBC, saying, "I got big hands, man. I would hurt her, you know? It would be more than just a little cut on the lip."
Brown further described the incident as a "little spat." He said the two were playfully "slap boxing" and Houston took one of his jabs a "little serious."
Houston's publicist in Los Angeles, Nancy Seltzer, did not return messages left by the Associated Press.
Brown has been jailed twice this year. In February, he spent a month in jail for multiple probation violations before being released a month early for a March child-support hearing in Massachusetts. There, he spent another night in jail before paying a former lover more than $60,000 in back child-support payments.
Brown and Houston have been married since 1992 and have a 10-year-old daughter, Bobbi Kristina.
On Tuesday, Brown fired his previous attorney, Vincent Dimmock.
Dimmock hadn't received any payments from Brown since February, when he began representing the singer. Dimmock would not say how much money was owed, the attorney said Wednesday.
"I sincerely wish him the best," Dimmock said.