Dan Kennedy kept his side in the game, but it ultimately wasn't enough as Hainault's last-gasp effort sealed the win for Houston.
Chivas USA goalkeeper Dan Kennedy made a number of key saves throughout the match, but ultimately, last season's Eastern Conference champions found a very late breakthrough.
The home side's best chance came with five minutes left in the first half when Juan Pablo Angel's volley off a corner kick struck the near post with Houston goalkeeper Tally Hall stranded.
Houston had a great chance to take the lead in the 78th minute when Brad Davis sent a ball over the top of Chivas' defense that was met by a fantastic Brian Ching volley, only for it to rattle off the inside of the far post.
Just when it looked like the game would end scoreless, Houston found itself a winner.
Davis swung in a corner in the 92nd minute, which Kennedy punched away. Adam Moffat hit a shot from the top of the box and Hainault stuck out a foot to intercept, then turned and fired home from close range, leaving Kennedy with no chance and sealing all three points.
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