Milner's milestone moment came when he was introduced as a substitute for Carlos Baleba in the first half at Villa Park.
The 40-year-old has drawn level with former Villa and Manchester City midfielder Gareth Barry for the most games played in the Premier League.
Saluting Milner's achievement, Brighton boss Fabian Hurzeler said: "It is a special night for James. It's no coincidence that he's still proving he can play in the Premier League.
"It's a pleasure to work with him and have him in our squad as a player and role model."
Milner's landmark feat couldn't stop spluttering Brighton suffering another defeat as Jack Hinshelwood's 86th-minute own goal gifted the points to Villa.
Of Milner's 653 appearances, 435 have been starts and 218 from the bench.
A Premier League champion with Liverpool and Manchester City, Milner has made 15 top-flight appearances this season, with 13 as a substitute.
Milner, who made his debut with Leeds in 2002, would break the record if he appears in Brighton's next league game at Brentford on February 21st.