It was the second straight game Howard has missed with the injury. He is day to day.
Howard said he had a procedure Tuesday to have fluid drained from a cyst in the ankle, according to the Houston Chronicle.
"There's nothing wrong with my ankle per se, but the cyst caused some problems, caused a lot of pain that I've been feeling for about 2½ weeks," Howard said, according to the Houston newspaper.
He was the only Rockets player to start all 66 games this season before his injury kept him out for the first time on Monday.
"After the Miami game I couldn't walk," said Howard, referring to Sunday's loss to the host Heat, according to the Chronicle. "I just wanted to go make sure everything was OK in it. That's when I found out I had a cyst in it. We got some of that removed ... and I feel a lot better. My ankle is fine."
Howard, in his first season with Houston, is averaging 18.6 points, and his 12.4 rebounds per game rank fourth in the NBA.
Omer Asik started in his place Thursday night.
Information from The Associated Press was used in this report.