The Tech 3 Yamaha rider qualified an excellent second on the grid for the season-opener and enjoyed a good battle for a top-three spot with the Repsol Hondas of Marc Marquez and Dani Pedrosa.
But the 27-year-old Coventry rider was noticeably down on power compared to the factory machines around him, and could not get ahead.
He then ran wide at turn one under pressure from a recovering Valentino Rossi and had to settle for fifth in a race won by defending champion Jorge Lorenzo.
Rossi came through to finish second and give Yamaha a one-two finish, while debutant Marquez and Pedrosa were third and fourth respectively.
Crutchlow said: "After the way I had been performing in practice and qualifying, finishing fifth is a little bit frustrating.
"My pace was promising and I think I would have deserved to be on the podium, but it was clear to see that I was lacking a bit of speed on the straight.
"That meant I had to push hard to close the gap in the corners and if we can resolve that small issue I've no doubt I can have the possibility to really challenge the guys at the front.
"The top four are the best riders on the best bikes but I pushed them as hard as I could until the small mistake stopped me."