At issue was a James Harden breakaway dunk with 7:50 remaining that would have given the Rockets a 104-89 lead. The ball whipped through the net and back over the rim before bouncing off, and the officiating crew mistakenly ruled that Harden missed the dunk and denied Houston coach Mike D'Antoni's attempt to challenge the call.
In its appeal, Houston had contested that Harden's dunk not being counted as a basket was a misapplication of rules resulting in an incorrect score and not a judgment call by officials.
In its ruling, the NBA agreed with the Rockets' contention that referees misapplied the rules. However, commissioner Adam Silver determined that the Rockets had sufficient time to overcome the error "during the remainder of the fourth quarter and two subsequent overtime periods and thus the extraordinary remedy of granting a game protest was not warranted."
D'Antoni said he wasn't upset about the protest being denied because he didn't think the Rockets were likely to win it.
"It is what it is," he said.
The Rockets were leading 102-89 when officials waved off the dunk, but San Antonio rallied after the botched call.
Houston guard Austin Rivers said the decision wasn't a big deal since the call wasn't why the Rockets lost.
"We had plenty of chances to win the game,'' he said. "So whether that went in or went out, the Spurs did a great job of continuing to play basketball and we did a bad job of not finishing the game.''
The NBA has granted only three protests filed by teams in league history.
The league did announce that it has disciplined all three referees from the game for misapplying the coach's challenge rule. The NBA also said it will work with its competition committee to develop procedures to ensure the situation does not reoccur.
D'Antoni was unhappy the officials were disciplined.
"I hate it for them,'' he said. "They just made a mistake. We all make mistakes. So I hate it. That's probably the worst part of it. They're trying to get it right, and I'm sure they had good intentions.''
The Associated Press contributed to this report.