Bautista penned a one-year contract following his departure from Rizla Suzuki, and joins a Gresini team still regrouping following the tragic death of lead rider Marco Simoncelli at the recent Malaysian Grand Prix.
The 26-year-old Spaniard, who made the step up to the premier class with Suzuki in 2010 and has a best finish of fifth place to his name, tested for his new team at Valencia on Wednesday.
Team boss Fausto Gresini said: "I am particularly satisfied that Alvaro Bautista will ride a Honda RC213V in the colours of Team San Carlo Honda Gresini next year.
"He is a very fast rider and I also hold him in high regard for his personality and pleasant nature.
"I am sure that he will integrate swiftly into our group and that we will enjoy some pleasant experiences together in the future."
Bautista scored 152 points in 32 MotoGP starts for Suzuki and expressed his regret at his departure.
"I am very sad to be leaving Suzuki after the two great years that I have had here," he said.
"It has been a great team to work in and I have learnt a lot of things from everyone in the team."
Suzuki, who ran just one bike in the 2011 season, could turn to Randy de Puniet to fill the gap left by Bautista's departure, after the Frenchman impressed in a hastily-arranged test for the team in Valencia. De Puniet is a free agent after leaving Pramac Ducati.