The matchup will be ruled a no-contest and won't be rescheduled, per Big Ten policies.
"The health and safety of our student-athletes, coaches, and staff continue to be our main priority," athletic director Mark Coyle said in a statement. "The last couple of days have shown a decrease in positive cases, but not to the point where we are able to return to competition.
"We are disappointed not to be able to compete against Northwestern on Saturday, but we need to continue to focus on following all CDC and MDH guidelines and slow the spread of the virus."
Minnesota revealed Saturday that it received 40 positive COVID-19 tests since Nov. 19, which included 20 infected players.
The program suspended all football activities last Tuesday, and its previous game Saturday against Wisconsin was called off due to the virus outbreak.
As a result of this week's cancellation, Northwestern will clinch the Big Ten West and therefore play in the conference championship game, according to CBS Sports' Jerry Palm.
The Golden Gophers' next contest is scheduled for Dec. 12 at Nebraska.