Gobert contested Williams on a drive to the rim with 9:22 to go in the second quarter, causing Williams to fall to the ground. Gobert tripped over Williams and while down on the court appeared to sweep a leg out in an attempt to trip Williams when the Thunder forward was attempting to get up.
A brief scuffle ensued, after which Gobert was assessed a flagrant foul 2 and ejected. Williams received a technical foul.
"I trust that they got it right," Thunder coach Mark Daigneault said of the officials' ruling.
Gobert finished with six points and four rebounds in nine minutes. It was the fifth ejection of his career.
The game continued to be chippy after Gobert's exit, with both teams combining for eight technical fouls, five on Minnesota.
"The frustrations boiled over," Timberwolves coach Chris Finch said. "It was not the most mature effort by us."
Minus their center, the Timberwolves allowed the Thunder to shoot 51.6% from the field and score 66 points in the paint.
Minnesota is already short-handed in the frontcourt, with All-Star forward Karl-Anthony Towns sidelined indefinitely with a calf injury.
The Associated Press contributed to this report.