With just three races of the season left, Lorenzo can now afford to finish third in each one and still take the title - even if Pedrosa takes three wins.
And Lorenzo's remarkable consistency - he has finished in the top two of every race apart from Assen, where he crashed out - makes him favourite to regain the title he won in 2010.
Japan MotoGP: top three riders
Crutchlow said: "All I can do after the way the race finished is take the positives from this weekend and there are a lot.
"There is no denying that I am disappointed as well because I was confident I could have passed Alvaro on the last lap. It wouldn't have been easy because he was riding very well and it was a very enjoyable battle with him.
"I had a lot of fun and I'm sure he did too and it is just unfortunate that we couldn't take the fight right to the very end. Even fourth would have been good for my hopes of finishing fifth in the Championship but I lost a lot of points today.
"We knew fuel consumption was going to be critical. I was very fast and for almost the whole race I was on my own with no slipstream, so I used more fuel.
"I've proven again though that I can fight with the best in the world."
Pedrosa got off to his usual strong start from second on the grid and made a move to pass Lorenzo at turn one, only for the Yamaha rider to cut across and strongly defend his position.
Lorenzo's team-mate Ben Spies then crashed out of third at the start of lap two before the front two pulled out a two-second advantage over Crutchlow.
Stoner briefly threatened to mount a podium challenge but faded as the race drew on.
Crutchlow saved a big slide in the closing stages before Bautista passed him with an aggressive move, only for the Briton to fight back into third spot with three laps left.
The pair touched but Crutchlow's hopes of a second MotoGP podium were dashed on the last lap when he suddenly slowed and had to pull off and retire. He then hitched a lift back to the pits on the back of Lorenzo's bike
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