Ant Danylyk used the game to give some of his squad who had been sitting on the bench of late some game time and starts were handed to the likes of MacKenzie Faulkner, Ricky Bridge, Sam Grimshaw, Rob Stevenson and Toby Mullarkey.
Niall Maguire had an early chance when his close range header from a corner dropped the wrong side of the post.
Ti Grice then had a shot saved by the keeper’s legs whilst ben Chapman in the Blues goal was relatively untroubled in the first half.
The Scholars went in front on 52 minutes when former Blue Rhys Thompson collected a superb pass and cut into the penalty area from the left firing past Chapman.
It was 2-0 six minutes later when Mitch Piggon hit a fine low stikre into the bottom corner of the net.
Blues tried to reduce the arrears but were denied by a great double save from Tom France and Grimshaw.
Tim Grice dragged a shot wide when well-placed and substitute Chris Budrys saw his shot saved when one-on-one with the keeper but Chasetown saw the match out to progress to the next round.
Team: Chapman, Faulkner, Bridge, Maguire (Morris, 74), Smith, Mullarkey, France (Johnson, 69), Shelley, Grice (Budrys, 74), Stevenson, Grimshaw
Unused subs: Curley, Danylyk
Attendance: 93