Van Gerwen has previously been defeated in two Sydney Darts Masters finals and at the 2014 Perth Darts Masters since the PDC introduced the World Series of Darts three years ago, but went all the way this time as he also denied Chisnall a maiden TV triumph.
Chisnall had followed up Friday's superb 10-7 quarter-final win over World Champion Gary Anderson with a brilliant display to see off Raymond van Barneveld 11-8 in their semi-final in Perth.
However, he once again saw his hopes shattered by van Gerwen as the world number one bounced back from last week's loss to Phil Taylor in Sydney in style, taking a ninth straight win against Chisnall and his 14th tournament victory of 2016.
The Dutchman had earlier swept aside Peter Wright 11-5 in the semis, winning five successive legs early on to move into an advantage he would never lose, and after taking a 4-1 lead in the final against Chisnall was always on course to claim the win.
Chisnall hit back to 5-3 before the Dutchman took three in a row, including an 11-darter, to edge towards victory, and though the Englishman pulled a leg back he was unable to continue his challenge as van Gerwen completed the triumph.
"This is my first World Series win in Australia so it's a great victory," said van Gerwen. "Dave's such a good player and you have to produce your best game but I went into the final with a lot of confidence because I had a fantastic record against him.
"I found it hard and didn't play my best game, but think I did well to win this trophy and I'm glad I did.
"I think tonight I played well; against Peter Wright I didn't give him any chances and against Dave I did the right thing at the right moments, and if you want to win the tournament you have to do that."
Chisnall won past the semi-finals for the first time in five attempts on the World Series of Darts circuit, hitting eight 180s and averaging almost 105 in his win over van Barneveld.
However, he lost in a televised final against van Gerwen for the second time this year, following January's loss in the Unibet Masters, and admitted: "Michael showed why he's world number one - he's a great player.
"I've played Michael a lot of times and he does what he does. He wasn't in his best form tonight but he still wins, he hits the right scores at the right times.
"I tried my hardest and it wasn't good enough, but I'll work on it like I always do. I've had a great weekend and I'm happy - I'll take a lot of confidence from this week."
The defeat for van Barneveld saw him lose out in the semi-finals for a second time on the World Series circuit in 2016, after defeating Simon Whitlock and Adrian Lewis earlier in the weekend in Perth.
Wright, meanwhile, was left to rue a second semi-final defeat to van Gerwen in as many weeks as he once again missed out - but having produced one of his finest-ever displays in Friday's quarter-final defeat to Corey Cadby was left to rue missed doubles against the Dutchman.
Van Gerwen's win means that he now enters November's Ladbrokes World Series of Darts Finals as the number one seed, after jumping above Anderson in the World Series rankings with his win in Perth.
The Ladbrokes World Series of Darts Finals will be held on November 5-6 at the Braehead Arena in Glasgow. For tickets visit www.ticketmaster.co.uk or call 0844 499 1700 .