The 38-year-old Queenslander missed the cut at the British Open last week and pulled out during the first round of the US Open on June 18, again with an injured back.
The 3M withdrawal is a setback for the former world No.1, who is currently 72nd in the FedEx Cup standings with just three events remaining in the PGA Tour's regular season.
Day, a 13-time winner on the PGA Tour, has managed just two top-10 finishes this season and sits 56th in the Official World Golf Rankings.
Veteran Charley Hoffman has replaced him in the field for the 3M Open, which begins on Thursday at TPC Twin Cities in Blaine, Minnesota.
Scottie Scheffler headlines as a debutant and continues the trend of playing the week following a major championship in 2026. He is the first world No.1 to compete at the event since Brooks Koepka in 2019.
Scheffler, the No.1 player in the FedExCup standings, lost in a play-off both at the RBC Heritage after the Masters and at the Travelers Championship the week after the US Open.
Coming off a tied fourth-place finish at the British Open, he said he has added the 3M to his calendar because he didn't want to take time off with the Tour playoffs looming next month.
Scheffler's fellow American, Kurt Kitayama, returns to defend the title he bagged last year with a one-shot victory over countryman Sam Stevens.
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