In the final session, however, they were overshadowed by their fellow England opener Mark Butcher who took three wickets for two runs in 14 balls as Lancashire, who were 95 without loss, slipped to 98 for 3, still six runs short of wiping off their first-innings deficit.
Atherton was first out, trapped lbw by Butcher after a confident 105- ball 53. Butcher then removed Mark Chilton and his opposing captain, John Crawley, caught behind for a duck.
Earlier Stewart's 95 was the centrepiece of Surrey's 298 as they built a first innings lead of 104. His timing and placement seemed to be somewhere near his best, as he tore into the Lancashire attack.
Robin Smith, the Hampshire captain, hit 78 in response to Leicestershire's formidable first innings total of 405 at Southampton. Smith was one of three Hampshire players to record half centuries as they finished the second day 161 behind, but comfortably placed at 239 for 4.