His runs came on the same day as his younger brother Grant, himself a long serving Zimbabwe Test batsman, appeared to have taken part in a player boycott of a leading fixture in the troubled African state.
Warwickshire's Ian Bell, long touted as a Test prospect, was 70 not out off 117 balls in the earliest start to an English season, beating last year's mark by three days.
But left-hander Flower contributed a typically effective 40 off 65 balls with six fours, sharing an unbroken fourth wicket stand of 95 with England's Bell.
Sussex were bowled out for a meagre score after winning the toss, opener Richard Montgomerie's 61 the only significant score with former Zimbabwe batsman Murray Goodwin managing a mere 17.
Kent off-spinner James Tredwell led the bowling with three for 20, including a spell of three for eight in 13 balls, although he was assisted by some rash shots from the Sussex batsmen. Essex seamer Graham Napier took three for 38.
Flower, 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, where they play Sheffield Shield cricket for South Australia and Western Australia respectively.
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.
The duo's former Test teammate Heath Streak is currently engaged in a dispute with the Zimbabwe Cricket Union after being axed from the Test captaincy.
In Zimbabwe, Grant Flower failed to appear in a Logan Cup match - the country's premier domestic competition - for Mashonaland against Midlands in the central town of Kwekwe.
Test allrounder Andy Blignaut was also absent after the pair had sat by Streak and lawyer Chris Ventura for five-and-a-half hours as efforts to solve the impasse over Streak's removal as captain proved fruitless.
MCC, managed by England selector Rod Marsh, the former Australia wicketkeeper, are fielding a team largely made up of England hopefuls.