Pity Martinez scored in the 89th minute and Josef Martinez added the insurance goal in stoppage time as second place Atlanta improved to 11-8-3 on the MLS season.
Guzan stopped three shots for the shutout over D.C. United, who missed Rooney as they rely heavily on him for much of their scoring. Guzan now has a league-leading 10 shutouts.
D.C.'s loss dropped them to third place in the Eastern Conference with a 9-6-8 record, one point back from Atlanta.
Rooney was left off the roster of the key regular season contest after coach Ben Olsen allowed him to take some time off due to some "niggling" injuries, about which he refused to go into detail.
As a result the 33-year-old Rooney missed his first match because of injuries since joining the MLS team last year.
"There are some signs of wear and tear, some little niggling things," Olsen said. "It's just time to give him a mental and physical break. It's that simple. It's not something we want to push right now."
Rooney leads the team in goals, with 11, and assists, with seven. He has been in on 58 percent of United's goals.
His goal total is tied for fourth in the league.