Jenson Button will be demoted five places on the grid after a change of gearbox for this weekend's Japanese Grand Prix.
The 32-year-old's car has the same problem that forced team-mate Lewis Hamilton to retire while leading in Singapore two weeks ago.
McLaren will fit new gearboxes to both cars but Hamilton will not be penalised because he failed to finish the race.
"This is a great disappointment for Jenson and the team," said McLaren technical director Paddy Lowe.
"On the positive side, we have understood and completely resolved the issue, allowing both drivers to compete with confidence for podium positions."
Button's title chances are virtually over, trailing Fernando Alonso by 75 points with six races remaining, but he has no shortage of motivation for this weekend's race in Japan, the country of his girlfriend Jessica Michibata.
"All of my grand prix wins have felt special, but winning at Suzuka in 2011, at the first grand prix held in Japan since the terrible tsunami last March, was an achievement that still makes me feel incredibly proud and emotional," said the Frome Flyer.
"Japan means a lot to me. It's a place I love, I've been there so many times – for business and pleasure – and I still feel that wide-eyed awe and deep emotion for a country that exists so comfortably on so many different levels.
"Suzuka is definitely a circuit that puts hair on your chest. It's extremely uncompromising, like a street circuit.
"It doesn't allow for a single mistake, punishing you for putting a wheel wrong at almost every point on the circuit.
"But it's also extremely quick – there's only one line through the esses that make up the whole first section.
"The Degner corners are blind, hidden in dips in the track, and approached over bumps that jolt the car, trying to unbalance it.
"Successfully hitting the apex for Degner 1 is a bit like trying to thread a needle while running the 100 metres."
Button will have a new team-mate at McLaren next season after Hamilton announced his departure last week.
He will be replaced by Mexican driver Sergio Perez, who is competing for Sauber this year and currently lies three places behind Button in the World Championship standings.