Santos, which lost the first leg to Houston 1-0, advances with a 3-1 aggregate and will next face the Seattle Sounders.
It was the Dynamo's fourth loss in five visits to Mexico.
Santos opened the scoring when Hall knocked the ball into his own net in the 23rd minute. Gomez made it 2-0 five minutes later and Marc Crosas finished the scoring in the 76th.
The Sounders defeated Mexico's Tigres 3-1 Tuesday and moved ahead on a 3-2 aggregate.