The Queenslander tied with Marcus Gronholm with a time of two minutes 57.5 seconds.
Sebastien Loeb was the third quickest, just 0.3 seconds behind Atkinson and Gronholm.
Henning Solberg was fourth fastest 1.4 seconds ahead of his brother, and Atkinson's team mate, Petter Solberg.
"Thats a good confidence booster," Atkinson said after the Shakedown.
"We have done a lot of work in preparation for this event so I'm really hoping for a good weekend."
Rally d’Italia-Sardegna will be the third gravel rally of the year, following Mexico and Argentina.
The official action on Friday morning at 0846hrs Italian time (1646 AEST) with the Terranova stage to the south of Olbia. Each Leg will feature three stages repeated twice and will cover a total competitive distance of 344.94 kilometres. The event will be concluded when the winning car crosses the finish ramp in Porto Cervo at 1415hrs (2215 AEST) on Sunday.
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