The French side topped the table with 70 points from their 33 matches, ahead of Tampines Rovers on 69.
"It's much more difficult for a foreign team to win because most Singaporeans are against us," the Stars' captain Matthias Verschave said after the decisive 4-2 win over Japan's Albirex Niigata.
Their triumph completed a first-season double for Etoile who also won the League Cup earlier in the year.
"I feel like my stomach is only half-full because we didn't 'makan' (eat) the Singapore Cup," Stars' chairman Johan Gouttefangeas joked.
Etoile's triumph was welcomed in some surprising quarters.
"Having a foreign champion is a good wake-up call for all local clubs," coach of last year's champions SAFFC, told the Straits Times newspaper.
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