Pramac Racing's Martin leads the championship with 366 points while Ducati's Bagnaia has 345. Marquez is fourth, 78 points behind Martin, after retiring from the Indonesian Grand Prix with engine trouble in a points-scoring position.
Marquez also said Enea Bastianini - who is three points ahead of him in third - is also probably out of the title race after crashing out seconds after setting the fastest lap in Mandalika.
"We already had a big deficit and after the zero points score in the Indonesian Grand Prix, the difference is now too much," Marquez told reporters ahead of this weekend's Japanese Grand Prix.
"The title has been our target for the last five races, but it looks like the championship is now game over for us. The gap is already too big and the title is a two-man race.
"This gives me the peace of mind to keep working on the weak points in the last races and confirm the strong ones."
Marquez is the only one among the top four riding last year's Ducati Desmosedici GP23, with the other three riding the newer GP24.
But the Spaniard, who is moving to the factory Ducati team next year, had slowly come to grips with the machine after making the switch from Honda prior to the 2024 season.
After a number of podiums, Marquez finally won his first race in 1,043 days when he took the chequered flag at the Aragon Grand Prix and followed it up with another win in San Marino.
But with five races left in the season, Marquez said he will now focus on improving his qualifying lap times after crashing out in Q2 in recent grands prix.
"I will try to, as I said before Mandalika and Misano, finish the season in a good way, by trying to find that consistency ...," he said.
"Let's see if we can fight for the podium."
