Aoyama was the last man to win the 250cc championship in 2009 before it switched to Moto2.
He then spent two years racing in MotoGP's premier class, first with the Interwetten and then the Gresini satellite Honda squads.
His best finish came at Jerez in 2011 when he finished fourth, beating Valentino Rossi - then in his first year with Ducati – on the way.
Avintia confirmed on Monday that Aoyama would stand in for the injured Hernandez in this year's finale, but has now moved to announce him full-time for next year's campaign.
"First of all I want to thank the Avintia Blusens team for giving me the opportunity to return to the MotoGP World Championship, where I have had my best results as a rider," Aoyama said.
"The team has worked hard this year to develop a new bike and have made great progress.
"I hope I can help continue the development of the bike and I am convinced that we can do good things together.
"I'm excited to get back into action in this category and test the CRT.
"I also want to thank the Honda World Superbike team for giving me permission to ride at the Valencian GP, despite having a contract with them until end of season.
"I will give the maximum next season, because recent years have not been very good for me. I return with great enthusiasm and am eager to show my full potential."
Avintia has struggled in its first season in CRT, with Hernandez 17th in the championship and able to boast less than half of lead CRT rider Aleix Espargaro's overall points.
Ivan Silva, meanwhile, has claimed just five points finishes across the season, with a best finish of 18th.
Avintia has not confirmed who will get the second seat in 2013.
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