Thomas was tied up along the sideline by Portland's Carmelo Anthony with 10:32 left in the quarter. As he broke away from Anthony, he made contact with referee Marat Kogut, who stumbled into the crowd.
Thomas was given a technical foul and ejected. The call was reviewed and upheld.
The Wizards went on to lose 122-103.
"He made physical contact with the referee,'' crew chief Mark Ayotte said in a pool report. "It was definitely just a push during the dead ball contact with the referee.''
Wizards coach Scott Brooks thought the contact was accidental.
"I mean, I had a different view of it, obviously," he said. "They were in a scrum and they were fighting for the ball, a jump ball. I had a view that it looked like he lost his balance, but [Kogut] had a better view and then they looked at it. They looked at it, so you would hope they made the right call.''
Thomas wasn't in the locker room after the game.
"I didn't really pay much attention to the contact and I was standing right there," Trail Blazers guard Damian Lillard said. "I thought he just fell into him. And that was it. They reviewed it and they kind of stood their ground on it. So I guess what they thought happened, happened.''
According to Elias Sports Bureau research, the previous player to be ejected within the first two minutes of an NBA game was Utah's Greg Ostertag on Dec. 8, 2002, against the Lakers in Los Angeles.
Thomas received a two-game suspension after walking into the stands to confront two fans following a timeout in Philadelphia on Dec. 21.
The Associated Press contributed to this report.