After Hussey won the toss and sent the Stars in to bat at the Melbourne Cricket Ground, the home side reached 176 for nine thanks largely to a scintillating 74 from English star Kevin Pietersen.
But Thunder's Usman Khawaja (70) played an innings of similar quality to get Sydney's run chase off to a perfect start. He and fellow opener Jacques Kallis (28) put on 86 before the South African holed out in the deep to Pietersen off Adam Zampa.
But Hussey, playing his final match in Australia, hit a quickfire 18 to get the Thunder back on track, and useful contributions from Aiden Blizzard (16) and Ben Rohrer (13 not out) got them home.
Hussey, whose younger brother David captained the Stars, said the win was the result of much groundwork.
"It's been a great journey -- we've been building something for the past few years so to reach the summit is something pretty special," he said.
"We've got a lot of all-rounders and when you've got three of the world's best allrounders (Kallis, Watson and Andre Russell), it makes the captain's job a lot easier."
Earlier, Pietersen played a lone hand for the Stars, smashing the ball all over the MCG as he raced to 74 from just 39 balls, including four boundaries and five massive sixes.
However he got little support from his teammates, with fellow Englishman Luke Wright the next highest scorer with 23.
When Pietersen was in full flight the Stars looked like setting a huge target for the Thunder to chase, but they lost wickets steadily and momentum slowed, despite a late flourish from Evan Gulbis (16) and Zampa (15).
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