The Monster Yamaha Tech 3 rider said his arm injury (severe abrasions) from Silverstone was not holding him back at the GP Aperol di San Marino e Riviera di Rimini, but he struggled for a good setting on Friday and then again on Saturday morning.
He made it through from Q1 to secure fifth on the grid in Q2 on Saturday as he made a big step forward on the afternoon, but he was unable to rediscover his podium form from earlier in the season as he contested fifth place throughout the race with Honda-equipped rival Stefan Bradl.
The Ducati-bound Brit eventually lost that battle on the last lap as Bradl made a calculated pass in the final stages and made it stick.
However, the Misano result - a ninth top sixth finish in 2013 - means Crutchlow remains comfortably the highest ranked non-factory rider in the World Championship standings on 146 points, 22 ahead Bradl.
"It is a shame that I lost fifth place on the last lap but it has been a very difficult weekend and I am happy to come away with this result," Crutchlow said afterwards.
"The top six is not what I am aiming for right now but I had no confidence with the bike all weekend, and it was important to get a strong finish. It was a very hard race because Stefan just sat on my back wheel from the first lap to the end and unfortunately he managed to find a way to pass me in the last corners."
The Englishman concluded,
"I tried my best to take fifth back but it wasn't meant to be, but I think the whole of the Monster Yamaha Tech 3 Team showed a lot of fighting qualities this weekend. My crew have never given up and they have worked really hard trying to build up my confidence and I am grateful for their support."