Yao scored 36 points, and the Rockets broke open a close game after Thomas was ejected to beat the New York Knicks 101-92 Wednesday night for their season-high fourth straight victory.
Rafer Alston added 20 points, eight assists and six rebounds for the Rockets, who seized control immediately after Thomas was tossed in the opening minute of the final quarter when he came onto the floor to argue with referee Eric Lewis that Yao should have been called for a 3-second violation.
It was unclear if the Knicks coach made contact with the official before he was thrown out for the first time this season, though he said he didn't. Going onto the floor doesn't warrant an automatic ejection.
The NBA will review the incident and likely interview Thomas and the officials.
"I was close enough in his ear that he could hear me, but I didn't bump him or anything like that," Thomas said. "The reaction that I gave, you can look at it two ways and say you could just give him a tech or he can be thrown out of the game. But I'm not a guy and I haven't shown in this league that I complain a lot.
"I think any time that you come on the floor like that, I think the official has ... you're really at the official's mercy. He can either call a technical foul on you or eject you, so he was well within his right to eject me from the game. But I would hope that in the future that they would understand that I don't normally walk out on the floor and say things unless I have a pretty valid complaint, at least in my mind."
Yao made the technical free throw to give Houston a 78-74 lead, then Luis Scola made a pair of buckets and Alston had a 3-pointer and another jumper in the decisive spurt, giving the Rockets an 87-76 advantage with 6:43 remaining.
The Rockets improved to 6-2 since All-Star guard Tracy McGrady went out of the lineup with a strained tendon in his left knee. Scola finished with 19 points, nine in the final quarter.
"Luis stepped up huge," Rockets coach Rick Adelman said. "He was the one that was going to be open because they were leaving him to go help on Yao. And he made the shots and he can get to the basket."
Jamal Crawford scored 21 points, Nate Robinson had 16 and Stephon Marbury 15 for the Knicks, who won Tuesday in Chicago but failed to match their season high of two straight victories.
The Rockets, who beat the Knicks five days ago in Houston, have won the last seven meetings, including five straight in New York. Yao added 11 rebounds and Chuck Hayes grabbed 13.
"The team has more confidence playing without T-Mac right now," Yao said. "That doesn't mean we don't need him. You have to face to those games when you don't have him. When you miss him, you still have to play. We're finding a way to play without him right now."
The Knicks overcame a dismal start to play the Rockets evenly for the first three quarters in the opener of a four-game homestand that probably determines if they have any realistic hope of keeping the bottom of the Eastern Conference playoff picture in sight.
The Knicks missed their first 12 shots and were down 10-0 before Quentin Richardson's two free throws 3½ minutes into the game brought a mock cheer from the crowd. New York didn't make a field goal until the period was half over, but trailed only 25-19 after Marbury made a layup as time expired.
The Rockets led most of the second quarter before the Knicks ran off 10 straight points, the final five from Crawford, to take a 48-43 lead with 1:23 remaining. Robinson banked in a 3-pointer over Yao to beat the buzzer and send New York to the break leading 53-50.
New York pushed the lead to six in the third quarter, but the Rockets tied it at 67 when Yao completed a three-point play after he was fouled while dunking over Malik Rose. Yao's two free throws with 9.4 seconds left gave Houston a 75-74 lead after three.
