Howard, who missed most of the preseason with injuries, returned after sitting out on Friday night.
"He had bouncy legs, you saw that from him," interim coach J.B. Bickerstaff said. "He was dominant tonight."
Howard felt the effects of getting a night off.
"I did feel pretty good tonight," Howard said. "The better shape I get in the better I'll be on the floor. I'll continue to work every day in practice to get in better shape."
Houston has won seven in a row against the Kings.
Howard also helped the Rockets by holding DeMarcus Cousins to 4-for-16 shooting. Cousins, who missed the first meeting with the Rockets because of an injury, was also hampered by foul trouble and finished with 14 points and nine rebounds. He fouled out with a little over two minutes left.
"I think the foul trouble bothered him from getting into a consistent type of rhythm," coach George Karl said.
Harden made a 3-pointer with about 90 seconds left to make it 115-109 and seal the win.
Ben McLemore scored 19 for the Kings.
"They just answered all of our pushes," Gay said. "We thought we had something going and they came back and hit a three, got a dunk or a layup or a foul. We just can't win like that."
Though Harden led the Rockets in scoring, he wasn't quite as dominant as he has been in recent meetings with the Kings. He entered the game averaging 41 points in the last four games against Sacramento, which included a career-high 51 points in April.
Houston has won five of its last six games after opening the season 5-10.
"We're playing better, playing as a team," Harden said. "Defensively we're playing really good."
The Rockets were down by one with about 7 1/2 minutes left when Harden drove into the lane and dished to Howard. But Howard's dunk try bounced off the rim and the Kings grabbed it.
Cousins made a pair of free throws on the other end to make it 98-95.
The Kings led by 3 before Ariza and Patrick Beverley made back to back 3-pointers to give Houston a 101-98 lead midway through the quarter. Harden blocked a shot by Darren Collison in between those baskets.
A jump shot by Marco Belinelli gave the Kings an 85-84 lead entering the fourth quarter.
The Rockets led by as many as 15 early, but a 34-point second quarter by the Kings cut the lead to 52-50 at halftime.
Kings: Belinelli received a flagrant 1 foul when he pushed Corey Brewer to the court as he drove to the basket in the fourth quarter. ... Collison had 18 points and Gay and Omri Casspi added 15 apiece.
D-MO'S RETURN: Houston's Donatas Motiejunas, who hasn't played since March, returned on Saturday night. The 7-footer has been out since surgery to repair a herniated disk and returned to practice earlier this week. Motiejunas drew a standing ovation when he entered the game for the first time with about 5 1/2 minutes left in the first quarter. He had one rebound and took a charge in about six minutes of play.
"It was shocking," he said. "Everything was so fast on the floor. It's going to take a little bit of time for me to get back into shape and get back in that position where I was last year. But I think it's just a matter of time."
WITHOUT WILLIE: It was Sacramento's first game without rookie Willie Cauley-Stein, who suffered an open dislocation of his right index finger against Boston. The sixth overall pick in this year's draft is expected to miss four to six weeks.
Kings: Visit Oklahoma City on Tuesday.
Rockets: Visit Brooklyn on Tuesday.
Jaylen Brown's 33 points leads Celtics to win vs. Cavs
Jaylen Brown goes for 33 points in 19 minutes as the Celtics cruise past the Cavaliers 141-103.
Hayward's clutch bucket wins it for the Hornets
Gordon Hayward runs down the clock and makes the driving layup to give the Hornets the lead with less than a second remaining.
Walker coasts through lane for finger roll
Lonnie Walker IV grabs the rebound, then goes coast to coast with little resistance for the layup.