A desperation three-pointer from 30 feet by Dame Lillard was off the mark, and the Bucks saw their four-game winning streak end.
Houston had a 30-25 lead after one quarter, but Milwaukee battled back to take a 59-57 lead into halftime.
The game had 14 lead changes and came down to the final minute as the Bucks missed opportunities to tie the game at the end.
Giannis Antetokounmpo led the Bucks with 27 points and 10 rebounds. Lillard added 22 points, and Brook Lopez and A.J. Green scored 12 points each, but it was not enough.
Milwaukee (32-25) will return home to play the Denver Nuggets at Fiserv Forum on Thursday at 7 p.m.
