Mr Flosse's Tahoeraa Huiraatira party won just over 45 per cent of the votes in Sunday's second round, ahead of incumbent Oscar Temaru's party.
Mr Temaru's UPLD won just over 29 percent of the vote, and Teva Rohfritsch, another candidate who used to have a close relationship with Mr Flosse, got 25.6 percent.
The French territory, which enjoys a high degree of autonomy, has seen 13 different governments rule in quick succession since 2004 when Mr Temaru first came to power.
Mr Temaru and Mr Flosse have largely dominated French Polynesia's political landscape since 2004.
The former was president five times during that time, and the Mr Flosse twice.
The victory of Mr Flosse, an old friend of former French president Jacques Chirac, is a significant defeat for Mr Temaru, who is seen as paying for the territory's dramatic economic and social crisis.
Unemployment in the territory, which has a population of 270,000, is estimated to be around 20 to 30 percent, and a fifth of the population lives below the poverty line.
Mr Temaru also confused voters by trying to register Polynesia on the UN's list of Non-Self-Governing Territories - a list of nations that the international body considers as colonised.