The ex-Formula One world champion started way down in 15th on the grid in his AMG Mercedes after Audi dominated qualifying by locking out the top six places in qualifying.
But he had a large slice of good fortune to thank as he made his final pit-stop before the safety car was deployed, which was enough to see the Finn leapfrog most of the field and claim an unlikely second win of the year and the third of his career.
Polesitter Mattias Ekstrom was the fastest man on the day in his Abt Audi and duly led the field until the safety car was sent out for a three-car accident that eliminated the Persson Mercedes of Britain's Gary Paffett, and the Audis of Martin Tomczyk and Christian Abt.
Ekstrom grabs birthday pole at Mugello
His second stop put him behind Hakkinen and try as he might, he could not find a way by his fellow Scandinavian on the undulating Tuscan circuit, finishing just three tenths of a second behind.
His result was though good enough to see him move into a 6.5 point championship lead ahead of defending title-holder, who was the last classified finisher in 11th.
Britain's Paul di Resta benefited from a great pit-stop from his Persson crew to take third place in his two-year-old Mercedes. He was comfortably ahead of Bruno Spengler's AMG machine.
The Canadian held up the Mucke-run version of Daniel la Rosa, the year-old Audis of Mike Rockenfeller and Alex Premat - the German making it past the Frenchman at turn one with three laps to go - and Tom Kristensen's Abt version.
Markus Winklehock – who was only named as a late replacement for Adam Carroll at TME Audi – was ninth with Susie Stoddart rounding out the top ten with her best finish of the season in a Mucke Mercedes.
Carroll dropped by TME