The 31-year-old spent two full seasons in grand prix racing's premier class following his 2009 250cc world championship triumph.
His best finish came in 2011 at Jerez, when he claimed fourth behind Jorge Lorenzo, Dani Pedrosa and Nicky Hayden.
This year Aoyama has competed in World Superbikes for Honda alongside Jonathan Rea, who was called up to replace Casey Stoner during the Australian's two-race injury lay-off.
Success has been in short supply however, with Aoyama just 18th in the standings.
He will contest the final MotoGP weekend in place of the injured Yonny Hernandez, who had been hoping to make the 2012 finale having also missed Phillip Island.
Aoyama will be the second replacement rider in MotoGP, following confirmation that Katsuyuki Nakasuga will stand in for the injured Ben Spies at Yamaha.
Across in Moto2, it has also been confirmed that Anthony West will not contest the Valencia finale.
The Australian's seat at QMMF had looked in doubt when he was suspended by the Federation Internationale de Motorcyclisme for a doping transgression.
Although he was given five days to appeal, the team has now confirmed he will be substituted by Indonesian rider Rafid Topan Sucipto.