The eight-time world champion took part in his final round with Honda in Valencia after 11 years with the Japanese marque and six titles in the premier class.
Ahead of his move to Gresini Ducati next year, Marquez was able to finish on the podium in the sprint race and felt he had the pace to do so again in the grand prix.
However, Marquez was taken out of the grand prix on lap six by Pramac's Jorge Martin.
"I would like to be better and start in a better way on Tuesday [in testing], but it was a big impact, especially on the head and the ankle," he began. "But nothing is broken, so this is the most important thing.
"And also the neck because I went into the gravel. But fortunately, this time it's not our mistake and we didn't finish in a good way or in the way I would like our relationship with Honda, because honestly speaking I approached the weekend like I was fighting for the championship.
"I was fully concentrated all the laps, all the races, all the practices. Yesterday we achieved the podium.
"Today, I don't like to say it but the podium was possible because the pace was there and I felt strong and I was managing the tyres."
Marquez added that Martin was "a bit too optimistic" in his overtaking attempt at Turn 4 when they collided, but understands his position and said it doesn't detract from the emotions of his final Honda round.
"Jorge was a bit too optimistic on that overtake, but I understand," he said.
"I will not push against him. I understand completely his mentality. I can imagine he was only looking at the red one [Francesco Bagnaia] in front far away and he was attacking.
"He already spoke to me and said sorry. But this doesn't change that the emotions of the weekend were super nice.
"We had a really nice… I don't want to say 'bye-bye' event, more like 'see you later' event with all the Honda staff. And today in the box there was also a lot of emotions."
