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The Italian broke the news via Twitter, saying: "I wish Giovanni the very best for his future, unfortunately our adventure together is over. Thanks a lot to him for his professionalism. Welcome back to my old friend and co-driver @LGranai. From now on he will be back by my side in the cockpit."
Bernacchini, who partnered Nasser Al-Attiyah to the WRC 2 title in 2014, joined Bertelli at the start of this season, replacing his former co-driver Mitia Dotta who quit to take up a job in Moto GP.
Luciano Finzi, vice coordinator of the FWRT team, denied the split was linked to the crash at last month's Vodafone Rallye de Portugal that left Bertelli in hospital overnight.
"It was only caused by a lack of feeling between him and Giovanni and the responsibility for the switch is not due to any of the two," he told wrc.com.
"Giovanni is without any doubt a great co-driver and a top level professional, but the feeling between driver and co-driver sometimes is not there."
Granai, 43, is a vastly experienced co-driver with a career that stretches back to 1997. He partnered Bertelli in his PWRC and WRC 2 campaigns between 2011 and 2013.