The reigning World Champion came for four tenths down on his team mate Nico Rosberg to set the quickest ever lap of the Bahrain International Circuit in Formula One.
Despite Hamilton's mega lap qualifying fell flat once again with all three sessions having between two and eight minutes of empty track action, which has increased calls to scrap the new format.
The Brit however escaped a penalty for reversing in the pit lane but the pole sitter was only handed a reprimand.
Q1 saw a shock first elimination with Felipe Nasr being the first car eliminated after making a mistake on his final run. The Brazilian was quickly followed by Rio Haryanto in the Manor. Jolyon Palmer briefly looked safe before Stoffel Vandoorne dropped the Brit in to the elimination zone.
Kevin Magnussen qualified 19th, despite having to start the race from the pit lane for missing the weighbridge in practice. The big shock of the session then came as Pascal Wehrlein moved his Manor to 16th dropping Sergio Perez into the elimination zone and out of qualifying.
The Mexican was joined by Marcus Ericsson who stayed in the pits along with Wehrlein. This meant the last three and a half minutes of Q1 had no cars out on track.
Q2 got off with a small drama after the session started but the green light failed to come on leaving effectively shortening the session by 60 seconds.
Nico Hulkenberg was only one of 3 cars that went out again and his lap saw both Toro Rosso's and Haas' Romain Grosjean knocked out as the German moved into Q3.
Both Williams went out again despite being comfortably through as Valtteri Bottas opted to start the race on a different set of Super Soft tyres.
However the session was also a flop, with eight and a half minutes of just two cars setting one flying lap each.
Q3 started on time and the first runs of the session saw Hamilton make a mistake at the final corner leaving him fourth with nine minutes remaining.
Nico Hulkenberg, Felipe Massa, his team mate Bottas and Daniel Ricciardo were the first four cars to be eliminated, leaving a Mercedes and Ferrari shootout for pole.
The second runs didn't go Ferrari's way with Raikkonen not improving and Vettel not improving enough, whereas the two Mercedes went even quicker and only being separated by 0.077.
Although Q3 was left with an empty two minutes, qualifying has set up the prospect of a great race tomorrow.
- Lewis Hamilton
- Nico Rosberg
- Sebastian Vettel
- Kimi Raikkonen
- Daniel Ricciardo
- Valtteri Bottas
- Felipe Massa
- Nico Hulkenberg
- Romain Grosjean
- Max Verstappen
- Carlos Sainz
- Stoffel Vandoorne
- Esterban Gutierrez
- Jenson Button
- Daniil Kvyat
- Pascal Wehrlein
- Marcus Ericsson
- Sergio Perez
- Kevin Magnussen
- Jolyon Palmer
- Rio Haryanto
- Felipe Nasr