
The victory in the penultimate weekend of the regular season capped a remarkable resurgence for DC United, who were languishing at the foot of the table when Rooney arrived in Washington in July.
Until that point, they had just two wins from 14 matches and appeared headed for another disappointing season.
They have since won 12 of 18 games to clinch their spot in the post-season.
Rooney opened the scoring in the eighth minute, tapping in his team-leading 11th goal of the season after Luciano Acosta eluded three New York defenders to reach the end line and cut the ball back to Rooney.
Acosta doubled DC’s lead in the 24th minute, curling in a strong shot from outside the area.
Rooney converted from the penalty spot in the 74th minute after Alex Ring handled the ball in the penalty box.
Spaniard David Villa pulled back a goal for New York in the 78th minute, but his low shot that went in off the far post wasn’t enough for a New York City FC side that had already punched their post-season ticket but are now struggling to hang onto third place in the Eastern Conference.