Rooney's 90th-minute penalty saw DC secure a 1-1 draw against New England Revolution at Gillette Stadium.
New England goalkeeper Matt Turner was sent off in the 56th minute after a heavy challenge on Rooney, but the hosts still took the lead through a Juan Agudelo header.
However, Rooney stepped up to convert a late spot-kick as DC United took a one-point lead atop the Eastern Conference.
Philadelphia could have moved top, but suffered a 3-1 loss at home to Portland Timbers.
Brian Fernandez scored a first-half brace, heading in an Andy Polo cross before completing a wonderful team move.
Diego Valeri's brilliant curling strike from 20 yards sealed Portland's win after Kacper Przybylko had pulled a goal back for Union.
The defeat ended Philadelphia's six-match unbeaten run.
Elsewhere, New York Red Bulls stretched its unbeaten streak to four games by beating FC Cincinnati 2-0.
Minnesota United edged Houston Dynamo 1-0, Vancouver Whitecaps overcame FC Dallas 2-1 and Chicago Fire drew 1-1 against New York City FC.
Nicolas Mezquida's late goal lifted Colorado Rapids to a 3-2 victory over Columbus Crew.