"I was like 'oh my bad.' I told him obviously, when we were running down the floor", Antetokounmpo told reporters. "I know by winning - doing whatever it takes out there, helping your teammates and just leaving it everything on the floor - everything will take care of itself".
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Antetokounmpo admitted later he apologized immediately to harden, and said it was an accident.
In-form Luka Doncic recorded 30 points as the Dallas Mavericks overcame the Phoenix Suns 104-94, while in Memphis, the Grizzlies stopped a six-game losing streak thanks to 26 points from Marc Gasol in their 96-86 win over the San Antonio Spurs.
Harden missed another 3 seconds later and the Bucks added four free throws down the stretch to secure the their seventh victory in eight games.
Antetokounmpo scored 27 points, claimed a career-high 21 rebounds and provided five assists at Toyota Center on Wednesday.
"He's not normal", Rockets coach Mike D'Antoni said.
Though Harden scored 42 points, he was just 13/30 from the field. Much of the third-quarter comeback was spearheaded by Malcolm Brogdon and Eric Bledsoe, and even on a cold night from Khris Middleton, it's clear Milwaukee is far from a one man show. Gerald Green chipped in 16 points off the bench.
The Bucks were down by 7 later in the quarter before using a 17-1 spurt to end the quarter and take a 92-83 lead into the fourth. It opened up an opportunity for Antetokounmpo to seal the deal by going on a personal 5-0 run.
Rockets: Chris Paul missed his ninth game in a row with a strained left hamstring. Houston shot 18 of 48 on 3-pointers.