Brady, who played in the team's preseason opener against the Saints, has sat out multiple exhibition games in the past, and head coach Bill Belichick had hinted at the possibility of giving him the night off in recent days.
Without Brady, the Patriots lost 27-17 to the Eagles.
In his place, second-year quarterback Ryan Mallett got the start, going 10 for 20 for 105 yards and a touchdown in the losing effort.
The team enters a stretch of three games in 10 days, and will also travel to Tampa Bay on Tuesday to participate in joint practices with the Buccaneers prior to Friday night's preseason game.
In addition to Brady, other players held out Monday night were linebacker Jerod Mayo, tight ends Rob Gronkowski and Aaron Hernandez, receivers Wes Welker and Brandon Lloyd and defensive lineman Vince Wilfork.
Field Yates is a contributor to ESPNBoston.com.