Gobert picked up his latest flagrant foul during the fourth quarter of Minnesota's 104-103 win over the San Antonio Spurs on Sunday.
Gobert was sanctioned after game officials ruled he had not given Spurs star Victor Wembanyama enough room to land safely after a three-point attempt.
The veteran told local media after the incident Sunday's foul had not been ill-intended.
"It's tough, because I try to be contesting shots in the heat of the moment," Gobert told the Minneapolis Star-Tribune.
"I don't think there's at any time an intention of getting anybody hurt or putting people in dangerous situations. It's tough. But got to play through it."
The 33-year-old will serve his suspension on Tuesday during the Timberwolves road game against the Milwaukee Bucks.