Nico Rosberg's third win in a row, from a sixth successive pole position, dashed Hamilton's hopes of a 44th career victory.
Nico Rosberg beat Lewis Hamilton to the top slot for the second year in a row by three tenths of a second.
Nico Rosberg lapped with a best time of one minute 41.983 seconds under the Yas Marina floodlights.
Lewis Hamilton chases his 44th win on 44th anniversary of the founding of the UAE in car 44.
Murali Vijay scored these 7,000 runs at an average of 46.05, including 17 hundreds, in 95 matches.
A 12th one-two finish from 19 races would be an icing on the cake for Mercedes.
Nico Rosberg and Lewis Hamilton had been separated by less than a second for 10 laps after the first pitstop but the gap then widened.
The F1 drivers will observe a minute of silence at the Brazilian GP in aftermath of Paris attacks.
Nico Rosberg again denied Lewis Hamilton a 50th career pole, this time by a mere 0.078 on a sunny afternoon at Interlagos.
The Force India pair of Nico Hulkenberg and Sergio Perez, the local hero and crowd favourite, finished seventh and eighth.
Jenson Button said he had no idea what it amounted to, was frustrated nonetheless with what has become a painfully familiar situation.
Nico Rosberg will hope Sunday's race breaks a bitter sequence after converting only two of his last 10 poles into victory.
Nico Rosberg lapped the Hermanos Rodriguez circuit with a best of one minute 21.531 seconds.
Nico Rosberg was adamant that Lewis Hamilton's move on Turn One was too aggressive to be acceptable.
An emotional Lewis Hamilton owed his victory, in the end, to an unforced error by Nico Rosberg on the 49th lap.
Nico Rosberg grabbed pole in a rain-shortened qualifying session while Mercedes team-mate Lewis Hamilton will start second.
Nico Rosberg lapped more than a second faster than anyone else, the German's best time of one minute 53.989 seconds.
Team technical director Nick Chester said initial investigations had not indicated anything broke on the car before the accident.
Lewis Hamilton is 66 points clear of Ferrari's Sebastian Vettel and 73 ahead of his own team mate Nico Rosberg.
Lewis Hamilton now has 302 points, Sebastian Vettel 236 and Nico Rosberg 229.
Nico Rosberg set an unbeatable time of 1 minute, 37.113 seconds midway through the final qualifying session in Sochi.
Carlos Sainz lost control of his car on a high-speed stretch heading into a steep right-hand corner, before scraping along the wall.
Fernando Alonso had triggered speculation after he told reporters last month that he did not know whether he would be in F1 next year.
Mercedes need to score just three points more than Ferrari in Sochi to retain the title they won at the inaugural Russian race last year.
Bernie Ecclestone did not name any of the interested parties.
McLaren had a termination clause in Jenson Button's contract that could have been triggered by the team this year.
Singapore had objected to having its September race back-to-back with neighbouring Malaysia.
Sebastian Vettel is 59 adrift of reigning champion Lewis Hamilton who chalked up his eighth win of the season in Japan on Sunday.
Lewis Hamilton and Nico Rosberg barely featured in television coverage after finishing one-two in Japanese GP.
Lewis Hamilton will surely win many more races in years to come but number 41 will always be special.
McLaren team boss says both Fernando Alonso and Jenson Button will continue to race for the team next season.
The win was the Lewis Hamilton's eighth of the season, with Nico Rosberg anchoring the eighth one-two finish for dominant Mercedes.
Nico Rosberg secured his first pole since Spain in May.
Rain also hit the morning session when Toro Rosso driver Carlos Sainz Jr. had the fastest time.
F1 returns to Suzuka where Marussia driver Jules Bianchi was seriously injured last year in an accident and eventually died.
Speculation about Jenson Button's future reached new heights after last Sunday's Singapore Grand Prix.