When the ejection was announced, Wembanyama appeared to ask Spurs team-mate Harrison Barnes: “What does that mean?”
Timberwolves’ victory on Sunday levels the best-of-seven series at 2-2 before game five in San Antonio, Texas on Tuesday.
Spurs coach Mitch Johnson said, while he did not condone Wembanyama’s actions, he was glad he “took matters into his own hands” as he believes the 7ft 4in (2.24m) star needs more protection from referees.
Johnson added: “I’m glad Naz Reid is OK and I didn’t want him to elbow him. But [Wembanyama’s] going to have to protect himself if no-one else does for him. And I think it’s disgusting.”
Wembanyama finished with four points and four rebounds in just under 13 minutes of action, while his Spurs team-mates De’Aaron Fox and Dylan Harper scored 24 points each.
Reid, meanwhile, contributed 15 points and nine rebounds off the bench for the Timberwolves.
“We never expected them just to go away,” Timberwolves coach Chris Finch said.
“They won a game in the Portland series without Wembanyama, so they’re a very good team.”
Also on Sunday, the New York Knicks advanced to the Eastern Conference finals as they brushed aside the Philadelphia 76ers 144-114 in game four.
Miles McBride scored 25 points and Jalen Brunson added 22 points to hand the Knicks a 4-0 series clean sweep.
The Knicks will take on top-seeded Detroit Pistons or fourth-seeded Cleveland Cavaliers for a spot in the NBA Finals.