Jenson Button will enter the Japanese Grand Prix knowing that he will drop five places on the grid from wherever he qualifies.
The 2009 world champion was beaten to pole position by Sebastian Vettel by 0.009s in the corresponding race in 2011 but went on to claim victory the following day.
With six races remaining, Button is 75 points adrift of Fernando Alonso in the world championship.
McLaren discovered the problem with Button's gearbox following the Singapore Grand Prix. Lewis Hamilton was forced to retire in Singapore with an identical issue.
"Jenson's gearbox had the same problem as Lewis's gearbox during the Singapore Grand Prix, and subsequent investigation has revealed a terminal failure", McLaren technical director Paddy Lowe told Autosport.
"Therefore both cars must start the Japanese Grand Prix with new gearboxes, which means that Jenson will receive a five-place penalty."
"Of course, this is a great disappointment for Jenson and the team. On the positive side, we have understood and completely resolved the issue, allowing both drivers to compete with confidence for podium positions."
Button has finished in the top eight at every race he has competed in at Suzuka.