Rain began to fall midway through Sunday's race at MotorLand, causing the majority of the riders to pit and change their bikes.
With only a handful of laps remaining, defending MotoGP champion Marquez - as well as team-mate Dani Pedrosa - elected to stay out on the Spanish circuit.
It was a gamble that failed to come off as both men spun off before recovering to finish 13th and 14th respectively as Yamaha's Jorge Lorenzo cruised to victory.
"It is not a race to forget, because I gained a lot of experience," said championship leader Marquez.
"Something like this had never happened. We were missing three or four laps and I thought to stay out because I was not losing too many seconds.
"But this time the risk has exceeded the limit. I did not know Pedrosa had fallen. I thought I could do it but this time the risk was too great.
"Eventually, however, we have had a good weekend and this is important."
Despite the disappointing finish for Marquez, Pedrosa's win means the defending champion extended his overall championship lead by one point to 75 with four races remaining.