The outcome means the two teams will meet again in an NFC wild-card contest next weekend, also at Arlington, Texas.
Romo passed for 311 yards, Felix Jones scored once on 15 carries for 91 yards and Marion Barber gained 91 yards on 14 attempts. The defense limited Philadelphia to 228 total yards in the Cowboys' second straight shutout -- a first for the proud franchise.
The Cowboys (11-5) will enter the playoffs with a three-game winning streak and will be the NFC's No. 3 seed behind New Orleans and Minnesota.
A 44-6 loss to Philadelphia in the 2008 regular-season finale left the Cowboys out of the playoffs.
Donovan McNabb passed for 223 yards without a touchdown, and Brent Celek caught seven passes for 96 yards for the Eagles (11-5), whose six-game winning streak ended.