Rooney's 90th-minute penalty saw D.C. 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 home side still took the lead through a Juan Agudelo header.
However, Rooney stepped up to convert a late spot-kick as United took a one-point lead atop the Eastern Conference.
Philadelphia could have moved top, but suffered a 3-1 loss at home to the Portland Timbers.
Brian Fernandez scored a first-half brace, heading in an Andy Polo cross before completing a wonderful team move for his and the club's second.
Diego Valeri's brilliant curling strike from 20 yards sealed Portland's win after Kacper Przybylko had pulled a goal back for the Union.
The defeat ended Philadelphia's six-match unbeaten run.
Elsewhere, the New York Red Bulls stretched their unbeaten streak to four games by beating Cincinnati 2-0, though they left it late.
Kaku opened the scoring 78 minutes in with Omir Fernandez putting the match to bed in stoppage time.
Tommy Smith and Pedro Santos traded goals in the first half hour with Jonathan Lewis netting just before halftime to send the Rapids to the break with a 2-1 lead.
Gyasi Zardes pulled the Crew back level before the hour mark only for Mezquida to net the winner in the final minutes of regular time.