Favre did not play for the second time in three weeks because of injury. He sat out a Dec. 13 game against the New York Giants because of an injured right shoulder, ending his record consecutive-starts streak at 297, dating back to 1992.
The 41-year-old Favre suffered a concussion last week against the Chicago Bears and was listed as doubtful.
Joe Webb made his first career NFL start.
Not even an extra 48 hours could help Favre. The Vikings-Eagles game was switched from Sunday night to Tuesday night because of a winter storm.
Vikings interim coach Leslie Frazier said on Monday that Favre still hadn't passed initial testing.
While the delay didn't help Favre, it allowed running back Adrian Peterson's bruised thigh to heal enough for Peterson to suit up Tuesday night.
Peterson injured his left thigh two weeks ago when he collided with quarterback Tarvaris Jackson on a handoff. He missed the game against Chicago, the first time he's sat out since missing two games with a knee injury his rookie season in 2006.
Information from The Associated Press contributed to this report.