Lee contributed 15 points and 13 rebounds. Klay Thompson and Stephen Curry each added 14 points for the Warriors.
Golden State posted a rare win over the Rockets, improving to 2-12 against them in 14 meetings while winning for the fourth time in six contests overall.
The Rockets, meanwhile, struggled to find the range in the fifth contest of their current six-game road trip, shooting just 41 percent from the field.
Kevin Martin scored 28 points to lead Houston.