Howard and childhood friend Josh Smith dominated early in the fourth quarter to help the Rockets pull away.
The Mavericks scored the first four points of the fourth quarter to take a three-point lead. But with Harden on the bench, Houston scored the next 11 points, powered by three alley-oop passes from Smith to Howard, to take a 92-84 lead with about 8 minutes left.
Smith, who connected with Howard on six alley-oop passes, finished with 15 points, nine assists and eight rebounds.
Monta Ellis had 24 points for Dallas, but big men Dirk Nowitzki and Tyson Chandler combined for just 21 points.
Game 3 is in Dallas on Friday night.