Flower, a former Zimbabwe skipper, now playing County cricket in England for Essex, had long been pencilled in to lead MCC in a revival of a fixture last played in 1991 when Middlesex were the reigning County champions.
But Goodwin was a late call-up to lead Sussex - who won the title for the first time in their history last season - after regular skipper Chris Adams withdrew because of an elbow injury.
Both Flower and Goodwin now divide their time between playing first-class cricket in England and Australia.
Flower represents South Australia while Goodwin Western Australia in the Sheffield Shield.
Goodwin, 31, a top-order batsman made his last international apperance in 2000 but quit in order to pursue a more lucrative first-class career.
Flower, 35, a mainstay of Zimbabwe's batting and often their wicketkeeper, retired from international cricket after last year's World Cup where, together with teammate Henry Olonga, he staged a black armband protest mourning the "death of democracy" in the African State under President Robert Mugabe.
Flower and Goodwin's former Test teammate Heath Streak is currently engaged in a dispute with the Zimbabwe Cricket Union (ZCU) after being axed from the Test captaincy.
MCC, managed by England selector and former Australia keeper Rod Marsh, are fielding a team largely made up of England hopefuls.