Colorado (7-9-9) hasn't lost to Houston (8-10-8) since 2009, winning five of the nine meetings.
Doyle climbed over a defender to head home Sean St Ledger's chipped cross. St Ledger started the sequence by running down a loose ball at the baseline and just got a foot on it before it went out of bounds.
Both teams were whistled for hand balls in the box in the first half, resulting in two penalty-kick goals.
Colorado's Vicente Sanchez started the scoring in the 20th minute after Alex touched the ball during a slide at the edge of the area. It was Colorado's first penalty kick conversion of the season.
Houston's Brad Davis tied it at 1 in the 37th after Bobby Burling deflected a cross with his hand.