Holden got his chance to break a 2-2 tie when Chicago's Brandon Prideaux was whistled for a foul on Corey Ashe.
The win was only the second in the past six games for the Western Conference leading Dynamo (11-6-5), while the Fire (8-4-8) had its five-game winning streak snapped.
Houston took a 2-0 lead in the first half on goals by Kei Kamara and Ricardo Clark. The Fire came back with goals by Chris Rolfe and Peter Lowry in the first three minutes of the second half to tie the match.
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