Martin endured a torrid grand prix in Qatar on Sunday, as a problem with his rear tyre meant he struggled to 10th while title rival Francesco Bagnaia finished second.
The Pramac rider is now 21 points adrift of Bagnaia in the championship, having cut his lead down to seven 24 hours earlier after winning the sprint, and later raged against Michelin for 'stealing' the title from him.
Martin found himself at one stage fighting with Honda's Marquez before the eight-time world champion eventually finished down in 11th.
Speaking after the race, Marquez said he could see Martin was struggling with rear grip but didn't want to fight him too hard as the points gained wouldn't have "changed my life".
"I did the whole race behind Martin," Marquez said. "At the beginning I saw that he was pulling hard and we were catching the group a little bit, but then I saw that he was starting to lose quite a bit of speed compared to the other Ducatis.
"He was suffering at the exit of the corners, I don't know what happened to him, he didn't have his usual speed.
"I didn't want to get into a battle with him at the end, it didn't change my life and he can use those few points."
He added: "When he passed me and I stuck with him I saw that Jorge didn't have the pace, many riders passed him, I made an attempt and I couldn't go either, so I decided to stay behind.
"He had Johann Zarco helping him, [which is] normal, he's his team-mate. I saw that with the race he had he was not able to concentrate and the problem was getting worse."
Marquez finished 11th in both races in Qatar having qualified in seventh, but conceded in the grand prix that he "couldn't ride well" and elected to ensure he got to the finish to better prepare himself for his final Honda outing in Valencia this weekend.
"It has been a better weekend than expected, we have been saving it, but logically in the race, both in the sprint and this Sunday the pace puts you in your place, and we have not had rhythm," he said.
"It's true that I couldn't ride well this Sunday, I wasn't at my best. I was strong on Saturday, but today I wasn't, and that made my race a bit calmer.
"It wouldn't have changed the position much either, so I went to finish the race to prepare for next weekend."
