Antetokounmpo was assessed a charging foul with 8:50 to go in the quarter, but went on to confront and headbutt Wagner during the dead ball situation.
The 2019 NBA MVP, who on Saturday was named as one of three finalists for the 2020 MVP award, was issued a flagrant two as a result of the headbutt and was subsequently ejected.
He had scored 12 points and hauled in nine rebounds prior to the ejection.
Bucks coach Mike Budenholzer said afterward that tension had been building all game between the teams.
"This is nothing new," Budenholzer said. "Giannis has been dealing with this for a long time. He is the MVP. He normally is phenomenal and today was a slip-up. In some ways it could be one of the best things that happened today as a learning moment. We will all remember that we have to keep our cool — players and coaches."
Milwaukee went on to defeat Washington 126-113 despite resting their four other starters for the whole game. With the No. 1 seed in the Eastern Conference locked up, it's possible Budenholzer was planning on resting Antetokounmpo for the regular season finale, anyway.
The Bucks play the Grizzlies in their final seeding game on Thursday. Tipoff is set for 4 p.m. ET.