The result finished Houston atop Group 3 with eight points, three better than Olimpia and five more than FAS of El Salvador.
The draw kept the Dymano unbeaten in 19 games since it opened BBVA Compass Stadium on May 12 and through 25 games at home since July 7, 2011.
Hainault made a near post run to deflect Nathan Sturgis in-swinging corner and stymie Olimpia's hopes of a second quarterfinal appearance in three years. It gave the United States a third team in the knockout round along with the LA Galaxy and Seattle Sounders.
Both sides finished the match without everybody that they started with.
Houston had to play the final 50 minutes without manager Dominic Kinnear.
He was dismissed by Guatemalan referee Juan Carlos Guerra apparently for berating the officiating crew after the Dynamo felt it should have been awarded a penalty when Calen Carr was knocked over by Israel Fonseca, and then Adrian Hainault was issued a yellow card for a foul on Douglas Caetano at midfield.
Olimpia finished with only 10 players after defender Brayan Beckeles was ejected in the 79th minute for a second yellow card - both for fouls on Carr.
Houston had more of the possession to start the game but Olimpia had the better chances, taking the lead in the 22nd minute when Caetano struck a right-footed free kick from 30 meters past goalkeeper Tyler Deric.
The Dynamo inserted Je-Vaughn Watson to start the second half and quickly began to generate better opportunities. Fabio DeSouza had to make a sliding block of Watson's cross inside the six in the 58th before Hainault's goal.
Houston continued to push forward after it equalized, getting a header by Cam Weaver off a cross from Carr to carom off the right post.
Both sides started the match without several of its regulars. Houston's leading scorers Will Bruin and Brad Davis did not dress, nor did midfielder Ricardo Clark. Olimpia was without Ramiro Bruschi and Irvin Reyna.
Olimpia needed only a victory to advance, but coming into the match had lost three straight away in the Champions League, four of its last five and had only one win in eight.