New England halted a three-game losing streak and the three points vaulted the Revolution (3-5-0) from ninth all the way to fourth in the Eastern Conference.
Sene forged a 1-1 tie in the 27th minute and then set up the game-winner from Fernando Cardenas in the final moments of the first half.
Colorado's goal came from Jaime Castrillon in the 21st minute. The Rapids (4-5-0) lost for the fourth time in five games.
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