Houston was denied eight times by Kennedy in normal time, and had another shot hit the post, but Andre Hainault finally found the net 2 minutes into stoppage time to give the Dynamo a 1-0 win over Chivas.
The Dynamo won their season opener for the first time since 2006, and captured three huge points in the first of seven road games to open the season.
Chivas failed to test Houston goalie Tally Hall as often, but had its chances, with Juan Pablo Angel finding the post late in the first half on the best one.
Houston lost the MLS Cup final last season at The Home Depot Center 1-0 to the Los Angeles Galaxy, but deserved to leave the stadium with a win this time.
Brian Ching and Will Bruin had the best scoring chances early in the game, but Chivas responded before half with two solid opportunities. Oswaldo Mindao sent an open header well of target, and Angel back-heeled off the post.
Angel had a penalty appeal denied early after half and both teams struggled to create solid chances until the midway point. Brad Davis fired wide left in the 70th for Houston, and Angel lifted an open header over the bar seconds later.
Kennedy continued to frustrate Houston with two quick saves, and was helped by the post in the 78th when Ching sent a half-volley off the left side.
Chivas survived the chances, many shots right at Kennedy, until 2 minutes into stoppage time. Adam Moffat took a shot from the edge of the area that sneaked through traffic to Hainault inside the area.
Hainault settled the ball and quickly turned and fired past a diving Kennedy, spoiling an otherwise solid effort from the Chivas goalie, who was under fire throughout the match.