Jones had 25 points by halftime, matching his previous career-best set on Wednesday, and James Harden added 22 points.
Houston led by 17 points before the Bucks got within six points in the third quarter. The Rockets responded with a big run to extend the lead and hold on for the victory.
Brandon Knight scored 26 points with seven assists for the NBA-worst Bucks, who have dropped eight in a row.
Jones received a standing ovation when he grabbed a rebound off a missed 3-pointer by O.J. Mayo and dribbled by him with a slick spin move before driving into the lane and finishing with an off-balance layup to push the lead to 112-97 with about 2 minutes remaining.
Dwight Howard added 20 points and 14 rebounds for the Rockets, Aaron Brooks had 10 points and four assists and Jones also had two blocks, a steal and an assist.
John Henson had 20 points and 15 rebounds for Milwaukee and Luke Ridnour added 14 points.
Houston led by 13 points with about 7 minutes left in the third quarter when Milwaukee went on a 9-2 run thanks to two 3-pointers by Knight and one by Ersan Ilyasova to cut the lead to 75-69.
The Rockets were up by seven soon after that when they scored nine straight points to push the lead to 89-73. Harden got that spurt going with a layup before Howard made two free throws before sinking a rare 3. The 6-foot-11 Howard, who often jokes that he should be allowed to shoot more 3s, smiled broadly and pointed at his teammates as he trotted down the court after hitting the long shot.
It was his second 3 this season and the fourth of his nine-year career.
The Bucks had three turnovers during that Houston run before ending their offensive drought by scoring the next five points. But Brooks swiped the ball from Knight after that, passed it to Harden, who finished with a two-handed slam to leave Houston up 91-78 entering the final period.
The Rockets bounced back from a tough loss to Oklahoma City on Thursday night in which they set an NBA record for the largest scoring differential between two halves by scoring 73 points in the first half and a franchise-low 19 after halftime.
They'd matched the 19 points they scored then with 5 minutes remaining in the first quarter en route to a 62-52 halftime lead.
Jones had five dunks in the first half and scored four points in the last 33 seconds of the half, capped by a nifty put back with 1.3 seconds left. He was particularly good in the second quarter when he was a perfect 7 for 7 from the field and made seven of his eight free throws for 21 points.
Jones played just 19 games as a rookie last season after being selected out of Kentucky with the 18th overall pick in the 2012 draft. He has appeared in 39 games this season with 34 starts. The 22-year-old Jones is the second-youngest Rocket to have a 30-point game behind Hakeem Olajuwon.
Notes: Milwaukee's Gary Neal missed the game with a stomach illness. . . . Ridnour got a technical midway through the second quarter and Larry Sanders got one in the third.