Berrettini, playing in his first tournament since injury, raced out the blocks to break Murray in just his second service game, before the Scot failed to capitalise on four break points in the following game.
A similar pattern continued for the remainder of the first set, with neither player able to capitalise on break-point opportunities before Berrettini claimed the 1-0 lead with a booming forehand down the line.
That was the first set that Murray had lost in the tournament and he responded by producing a gritty performance in the second.
Berrettini squandered three chances to break at 4-4 before a double fault in the tie-break handed Murray three set points, and the three-time grand slam champion duly obliged to level.
The Italian opened the decider with a break, with Murray requiring a medical timeout for a leg injury, and the world number 10 claimed victory after his opponent had required more treatment.
Berrettini added a second Stuttgart crown to his name, having lifted the title in 2019, while it was his third grass-court success.
The 26-year-old will look to carry that form into Wimbledon, which starts on June 27, while the injury will be of concern to Murray, who was denied his first title since 2019.
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