Benfeito, from Montreal, and Filion, from Laval, Que., were in third place entering the fifth and final dive, but they saved their best for last, leapfrogging England's Sarah Barrow and Tonia Couch, who got the silver medal, and Malaysia's Pandelela Rinong Pamg and Nur Dhabitah Sabri, who took the bronze.
The Canadians finished with a total of 310.65 points. The English team scored 307.92 and the Malaysians 300.12.
Benfeito and Filion have reached the podium in each of their eight international competitions together this year.
They were the bronze medallists at the 2012 Olympics and silver medallists at last year's world world championships.
Benfeito, 25, and Filion, 27, will also compete against each other in the individual 10-metre event.
Wednesday marked the first day of diving at the cosy Royal Commonwealth Pool in Edinburgh, about a 75-kilometre drive from Glasgow.