Nico Rosberg put Mercedes back on pole position while a violent crash for Daniil Kvyat meant a slightly early end to qualifying at the Suzuka circuit.
Having put their Singapore disappointment behind them, Mercedes went into Saturday's qualifying for the Japanese Grand Prix as the ones to beat.
Hamilton and Rosberg traded P1 in the opening two segments and it was all to play for in Q3.
Rosberg took the early advantage with a 1:32.584, however, it was a mere 0.076s quicker than Hamilton's time.
With the top ten all heading out for a second run, Daniil Kvyat crashed heavily. Drifting off the circuit, he touched the grass and entered a high-speed and violent crash in which he car spun and rolled. He walked away unhurt.
The red flags were brought out as a result and with the clock stopping with less than a minute remaining, Rosberg was handed pole position ahead of Hamilton.
Behind them Valtteri Bottas secured third place on the grid with Sebastian Vettel set to line up alongside him.
Felipe Massa and Kimi Raikkonen will make up the third row of the grid while Daniel Ricciardo is P7.
The Red Bull racer was unable to continue his form from FP3 in which he was the one to take the challenge to the Mercedes drivers. Instead he was overhauled by both Williams and Ferrari.
Romain Grosjean, Sergio Perez and Kvyat completed the top ten.
Meanwhile Jenson Button are arguably undone by a late yellow flag in Q1. On a hot lap the McLaren driver was forced to back off, as too were Felipe Nasr and others, when Max Verstappen's STR10 ground to a halt.
Verstappen qualified P15 as he was unable to take his place in Q2 while Alexander Rossi, who was only his only timed lap of the session when the yellow were waved, finished slowest of all.
1 Nico Rosberg Mercedes 1:32.584
2 Lewis Hamilton Mercedes 1:32.660 0.076
3 Valtteri Bottas Williams 1:33.024 0.440
4 Sebastian Vettel Ferrari 1:33.245 0.661
5 Felipe Massa Williams 1:33.337 0.753
6 Kimi Raikkonen Ferrari 1:33.347 0.763
7 Daniel Ricciardo Red Bull 1:33.497 0.913
8 Romain Grosjean Lotus 1:33.967 1.383
9 Sergio Perez Force India No time
10 Daniil Kvyat Red Bull No time
11 Nico Hulkenberg Force India 1:34.390
12 Carlos Sainz Toro Rosso 1:34.453
13 Pastor Maldonado Lotus 1:34.497
14 Fernando Alonso McLaren 1:34.785
15 Max Verstappen Toro Rosso No time
16 Jenson Button McLaren 1:35.664
17 Marcus Ericsson Sauber 1:35.673
18 Felipe Nasr Sauber 1:35.760
19 Will Stevens Manor 1:38.783
20 Alexander Rossi Manor 1:47.114