The hosts finished on 194 for six in their second innings after England were bowled out for 349 in their first, Anderson the pick of the touring side's bowling attack with the start of the first Ashes Test just nine days away.
Earlier, Kevin Pietersen was out for 122 and captain Andrew Flintoff 62 as England enjoyed some batting practice in the morning session.
Flintoff became the fourth England batsman to pass fifty before being bowled by Stuart Clark, and Pietersen was finally caught by Brett Lee off Nathan Bracken after hitting two sixes and 18 fours.
Wicketkeeper Geraint Jones was bowled by Australia fast bowler Glenn McGrath for 13, Ashley Giles bowled by Lee for nine and Steve Harmison bowled by Nathan Bracken for two.
McGrath finished with two for 63, Lee two for 57, Clark three for 50 and Bracken two for 51.
England took the wicket of first-innings centurion Phil Jaques in the first over of the hosts' second innings, Sajid Mahmood running the in-form opener out for four.
Ed Cowan was caught by Jones off Matthew Hoggard with the total on 18 before Simon Katich and Michael Clarke shared an untroubled century partnership in warm sunshine at the Sydney Cricket Ground.
Katich retired on 55 and Clarke, hoping for a place in the Australian Test side, went on to register his second half-century of the match before being bowled by spinner Ashley Giles for 68.
Anderson had Aaron O'Brien caught by Andrew Strauss at slip and bowled Daniel Smith first ball with a neat inswinger before trapping Moises Henriques lbw.
England have one more three-day warmup match before the first Test, against South Australia starting on Friday.