DC United captures consecutive MLS win
Dwayne De Rosario also scored for United (4-2-3). The Washington club is 4-0-3 in its last seven games.
Will Bruin scored twice for the Dynamo (2-2-2). Houston gave up three goals for the first time this season and is winless in its last four.
Houston has one more match left on its season-opening, seven-game trip before facing D.C. in the new BBVA Compass Stadium on May 12.
Santos, who has scored his team-leading six goals in the last six matches, put United ahead for good in the 70th minute on a powerful header of Daniel Woolard's cross. Goalkeeper Tally Hall go a palm on the effort, but could only push it off the underside of the crossbar and into the goal.
Houston pushed for a third equalizer, but United came closer to scoring late when De Rosario made a superb end-to-end run, only to be denied by Hall from close range.
Santos opened the scoring in the 11th minute when he headed in Chris Pontius's cross after Pontius reached Brandon McDonald's throughball and evaded Hall.
Bruin, who has scored his team-leading four goals during the past three matches, leveled it just after halftime by side-volleying in Jermaine Taylor's cross.
De Rosario put United ahead again in the 54th minute on a curling effort that just missed Pontius's head before bouncing off the post and in.
Bruin tied it again in the 59th minute on a shot that squirmed under Joe Willis' dive on a slick night.
United has 14 goals in their past six matches after scoring once in their first three.