Guintoli was aiming to return during the Italian round, but he has yet to make a full recovery from the broken ankle he sustained during the Tissot-Superpole 2 in Imola on May 1.
Canepa, who has competed in two rounds of the Superstock 1000 Cup this season and the Endurance World Championship, has been in action regularly over the last two seasons of the World Superbike Championship.
"I'm really happy to be back in WorldSBK and with the Pata Yamaha Official WorldSBK Team," Canepa said. "It is also great to have this opportunity in Italy and to race in front of the Italian fans.
"After completing the test with the Pata Yamaha team 10 days ago I feel ready to ride the WorldSBK-spec YZF-R1. For sure the level in the championship is very high but I will fight as usual to do my best."
Meanwhile, Alex Lowes will make his comeback for Pata Yamaha after missing the most recent event at Donington due to a broken clavicle he suffered in Race 2 at Sepang last month.
