Harmison bowled in the nets before the match but England decided to leave him out of the side with the start of the first Ashes Test against Australia just six days away.
Spinner Monty Panesar was included in the team in preference to Ashley Giles.
South Australia captain Darren Lehmann won the toss and chose to bat first in the three-day game, England's last before the first Test in Brisbane.
Martyn pulls out of tour game: Australia middle-order batsman Damien Martyn pulled out of his last warm-up match before the first Ashes Test today with an elbow injury.
Martyn was due to play for Western Australia against Queensland in an interstate one-day match in Perth but withdrew because of tendonitis in his elbow.
Team officials said the injury was not serious but the 35-year-old was ordered to rest as a precaution, Australian Associated Press reported.
Martyn was included in a 13-man Australian squad to play England in the first Ashes Test in Brisbane starting next week.