The Union improved to 9-0-0 at home and earned the first trophy since the franchise's expansion season in 2010.
Standout goalkeeper Andre Blake was out with a fractured right hand and 22-year-old Matt Freese earned the win, and his first career shutout, in his first appearance since July 3, 2019.
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The Revolution still managed to qualify for a play-in game to advance in the postseason.
New England failed to win in five tries against the Union this season.
In the 14th minute, Philadelphia's Ray Gaddis found himself wide open in the box but had his shot blocked. Gaddis has never scored in nine years in the league.
Following a free kick in the 27th minute, New England's Gustavo Bou collided with Freese just outside the goal area. Freese remained down for several minutes before play restarted.
The Revolution were awarded another free kick in the 38th minute from about 30 yards out after a foul was called on Alejandro Bedoya. But they were unable to capitalize as the kick was immediately cleared.
Bou dribbled in all alone in the 41st minute but had his cross blocked.
The Union went ahead 1-0 in the 42nd minute as Santos corralled a rebound and scored. The initial shot by Bedoya hit the crossbar and bounced out to Santos who tapped the shot in.
Philadelphia took a 2-0 advantage in the 69th minute when second half substitute Burke finished a cross by Jose Martinez.
In the 88th minute, Adam Buksa had his best scoring chance with a header in the box. But he shot the ball just high and over the net.