The 27-year-old will start from ninth on the grid at Suzuka, after being among a number of drivers to miss out on the chance to improve in the dying seconds of Q3 when Kimi Raikkonen's spun Lotus brought out the yellow flags.
But from the outset the McLaren driver was in difficulty, and could be heard on the radio telling his team he was expecting a "struggle".
To add to Hamilton's woes, Red Bull were in a class of their own during qualifying.
Sebastian Vettel took the 34th pole of his career, putting him behind only Michael Schumacher (68) and Ayrton Senna (65), with Mark Webber alongside him, although the reigning champion was reprimanded by the stewards for impeding championship leader Fernando Alonso during the frantic final seconds.
McLaren's disappointing performance comes after a recent run where the Woking-based team have had the fastest car on the grid, winning three of the last four races, starting from pole four times in a row.
The downturn does little to help Hamilton's effort to close a 52-point deficit to Ferrari's Alonso, who will start sixth, as well as keeping in touch with Vettel, who is homing in on the Spaniard at the top of the drivers' championship.
But, having by his own admission made an error on set-up, Hamilton knows he will need luck on his side if he is to have any hope of being close to the Red Bulls, who have had the car to beat in Japan.
He said: "The car was feeling good and was quick in FP2 and FP3 but I got it wrong in qualifying.
"Unfortunately as soon as you start qualifying, you are stuck with it and as soon as I did my first lap I knew immediately it was wrong.
"I did everything I could with my adjustments I have with the steering, I had the front wing maxed out and it was not enough to overcome the issue I had."
Hamilton knows his chances of victory are slim, and may well have to cross his fingers and hope Red Bull experience the sort of reliability issue that deprived Vettel a win in Valencia when the German was cruising to a 25-point haul.
"Sebastian all of a sudden has the quickest car this weekend and he had a quick car at the last race and got maximum points, he is probably the main competitor to Fernando but we still have six races to go, including on Sunday, and anything can happen in those races," he said.
"Maybe they won't finish those races and we will capitalise as a team, so we should never give up and we will keep pushing tomorrow [Sunday] and hope something magical happens."
Hamilton's team-mate Jenson Button will start eighth due to the five-place grid penalty he has to take due to a gearbox change.
Button set the third-fastest time and was far happier than Hamilton with his set-up and believes, with tyre degradation set to be a factor during the race, victory remains a possibility.
"We will see tomorrow [Sunday], their [Red Bull's] long runs did not look too impressive," said Button, whose penalty promoted home hero Kamui Kobayashi to third on the grid to the delight of the Suzuka crowd.
"In last year's race it was the rear tyres that caused problems, this year I think it will be all four tyres.
"From talking to other drivers on the grid they are struggling, as we might be, with blistering, graining, high tyre wear.
"So it's not going to be a straightforward race, if it was I think it would be very difficult to beat Red Bull but because it is so mixed in terms of strategy I think there is a possibility we can make up some places and, you never know, fight for the win."