Harden, who had 19 of his points in the third quarter, has at least 30 points and 10 assists in 18 games this season. The NBA's third-leading scorer entering the game, Harden finished two points shy of tying his career high. He was 16 for 28 from the field, including 6 for 11 from 3-point range, while making 13 of 14 free throws.
Nene added 21 points for the Rockets, who snapped a two-game skid while winning for just the fourth time in 10 games.
Embiid had 32 points and seven rebounds in his return to the lineup after missing the last two games with a knee contusion. Embiid, who was questionable until about 45 minutes before tipoff, showed that he was just fine with an emphatic, left-handed dunk over Nene for Philadelphia's first two points that drew loud cheers from the 76ers' large crowd.
It was also the 7-foot-2 center's first game since Thursday's announcement that he was not among the reserves chosen for the All-Star Game, which some in Philadelphia considered a snub.
The streaking 76ers lost for just the third time in the last 11 games.
The Rockets were without second-leading scorer Eric Gordon, who missed his second straight game with a back injury.
But the relentless Harden made up for Gordon's absence.
Houston snapped a 61-all halftime tie with a 12-0 run over the first 2:51 of the second half. Harden scored 10 of the points, including a dunk that made it 75-63. Houston's lead reached as high as 13 in the period, and the Rockets entered the fourth ahead 94-82 after Harden's step-back baseline jumper as time expired.
Embiid scored eight straight to open the fourth quarter, drawing roars from the capacity crowd that has become the new norm in Philadelphia these days after hitting his second straight 3-pointer to make it 94-90 with 10:47 to play. But the Rockets scored the next six points and Philadelphia never got closer than four the rest of the way.
Nik Stauskas pulled the 76ers within five at 117-112 with 52.8 seconds to play on a reverse layup. After a miss by Houston, Nene blocked Embiid's 3-point attempt with 20 seconds left to seal it.