The hosts beat Silverknowes 3&1 in the final of the double foursomes event, which involves 16 Capital clubs.
In a tight title decider, Mark Kernaghan and Kevin Cattanach finished two up on Jim Keggie and Callum McKinstry at the front.
And, at the back, Drew McIntosh and Donald Livingstone claimed a one-hole win over Jim Keggie and Keith Reilly.
Bruntsfield Links beat Swanston, Mortonhall and Dalmahoy to reach the final while Silverknowes defeated defending champions Royal Burgess, Baberton and Murrayfield in a brilliant run.
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“It was the first time since 2000 that Bruntsfield Links have won the Inter-Club….good home advantage!” said the club’s CEO, Michael Braidwood.
Mortonhall won the Edinburgh Ladies’ Inter-Club for the first time earlier in the year after beating fellow final debutants Turnhouse in the title decider at Kingsknowe.