The Ferrari driver arrived at Suzuka with a 29-point advantage over Red Bull's Sebastian Vettel, but a first-corner crash and a consummate triumph for his rival narrowed the gap to just four points with five races left.
Red Bull were the dominant force over the course of the weekend, as Vettel took a clean sweep of pole position, fastest lap and race win, while Ferrari's recent struggles continued.
Alonso started sixth on the grid, after being impeded by Vettel during qualifying, an offence his rival was reprimanded for, but did not make it beyond turn one.
The Spaniard made contact with the front wing of Kimi Raikkonen's Lotus as he edged to the outside on the run down to turn one, puncturing a rear tyre and sending the Ferrari into the gravel before coming to a halt in the middle of the track.
Vettel went on to cruise to a comfortable victory and on current form it is hard to see how Alonso can fend off the German's push for a third-straight title given Red Bull's edge in performance.
But the 31-year-old is determined to remain positive, despite his Suzuka setback.
"This result has practically wiped out the advantage I had before, but if I'd been told at the start of the season that we would have been in this situation five races from the end, I'd have happily signed for it," he said.
"We must work a lot on the development of the car. I'm not worried, but we must react to the step forward that the other competitors have made.
"Now we start a sort of mini-championship, run over five grands prix.
"The aim will be to score at least one point more than all the others. What happened to us today could happen to the others next time: the wheel turns and that is what races are all about."
The next round in Korea is just a week away, a race Vettel won comfortably in 2011.
Although he is now the favourite to secure the crown in the eyes of many, Vettel chose to strike a cautious note.
"I'm very careful. I think we had a long journey so far, and it's been a tough year," he said.
"Still there are many races to go so today I don't want to talk about the championship.
"I know I finished in front of everyone today, I won the race, so I know that I scored more points than anybody else today but you don't know what happens next weekend.
"I think we have a very tough remainder of the season with a very new calendar for all of us, with a lot of back-to-back races.
"Basically next week Korea, then two races, one in India and Abu Dhabi, and then obviously America and Sao Paulo.
"I think there's still a long way to go and as I said, we have to focus on every single race and try to do our best and then we will see whether it's good enough."
McLaren's Lewis Hamilton, after a weekend dominated by talk regarding his impending move to Mercedes, also closed the gap to Alonso as his fifth place narrowed his personal deficit to 42 points.
Hamilton never recovered from taking a wrong turn on set-up ahead of qualifying and he cut a downbeat figure with his title challenge fading.
"I am quite realistic, I know my situation, but the Red Bulls are going to be hard to beat," he said.
"I got some points but there is not much more I can be happy with.
"The fight is still on with Fernando not finishing so we will keep pushing."
He added: "Everyone should be concerned (by Red Bull's pace), they are very quick, they are always very quick in Korea and Sebastian has scored 50 points in the last two races, Fernando should be more worried than I am.
"I didn't get many points so the championship is not tight for me. I am a long way away, it's going to be very difficult but I will never give up and keep pushing and hopefully we will have a better weekend next weekend."