"The Process" picked on "the Beard" in the final seconds of the first half during the Sixers' 121-93 triumph on Monday at the Well-Fargo Center in Philadelphia.
"He's a great player," Embiid told reporters. "Obviously he can do a lot of stuff on the court. I have a lot of respect for him."
The Sixers led 65-50 when the Rockets stole a pass from J.J. Redick. Harden collected the ball on the break and led the Rockets in transition.
But Embiid trailed on the play. The Sixers big man ran behind Harden before he watched him put a shot up in the paint. Embiid then took flight, smacking Harden's shot into the backboard. He then glared back at Harden in celebration.
Harden scored a game-high 37 points and had six rebounds, three assists and two blocks in the loss. Embiid had 32 points and 14 rebounds for the Sixers.
"It's obviously great to go against great talent," Harden said. "Obviously you know how well Jo's been playing throughout the course of the season. He's a skilled big and so he kind of attacked us early."