Lorenzo headed into Sunday's race in Motegi 18 points behind Repsol Honda's brilliant rookie Marc Marquez and knew he needed to finish the GP - at worst - 24 points behind the 20-year-old if he was to maintain a tilt at the 2013 championship.
With 15 laps to go, Lorenzo had Marquez and Dani Pedrosa (also Repsol Honda) on his tail, but the two-time world champion managed to pull away in the closing stages to comfortably take the chequered flag.
Having started on pole, Lorenzo dominated the GP at the Twin Ring Motegi to win by 3.188 seconds over Marquez, while Pedrosa claimed third, 4.592s behind the Yamaha rider.
The win was Lorenzo's seventh of the year and second in a row, after he also took out the Australian GP at Phillip Island last week, and moved the 26-year-old Spaniard onto 305 points, while Marquez advanced to 318 with Pedrosa (280) in third overall.
"Until we finish racing, we know the championship is not over," Lorenzo said on www.motogp.com. "I'm not the leading rider, so it's not all up to me, so let's see how our strategy is at Valencia. I am the rider with the most victories in 2013 and that's very important."
If Marquez fails to claim any more points at the final race of the season in Valencia on November 10, Lorenzo will have to finish at least fourth to overhaul his compatriot.
If Lorenzo wins the GP in Spain, Marquez can remain top of the standings as long as he finishes in the top four.
Marquez will become the first rider to win the MotoGP title in his rookie season for 35 years if he can hold on in Valencia, and also become the youngest champion.
Honda Gresini's Alvaro Bautista finished fourth in Japan, almost 20 seconds behind Lorenzo, while Stefan Bradl of LCR Honda was fifth.
"Looking at the race classification all the top five after me were Honda riders and normally this track is better for them," Lorenzo added.
"So winning at Honda's home track with Yamaha's 200th victory in the MotoGP class, when we also took a risk with the soft tyre, was a pleasure.
"It was a hard race physically but I kept my concentration and I really wanted this victory."
Lorenzo's Yamaha team-mates Valentino Rossi took sixth position ahead of the Monster Yamaha Tech duo of Cal Crutchlow and Bradley Smith, while Nicky Hayden and Andrea Dovizioso completed the top 10.