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.
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 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.
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.
A charge sheet said Yogvitam Pravin Dhokia, 27, endangered the ‘personal safety of the drivers.’
A win in Singapore will take Lewis Hamilton’s tally to 41 wins from 161 races.
Lewis Hamilton now has a 53-point lead over teammate Nico Rosberg as the latter failed to finish the race.
Lewis Hamilton is just two wins away from matching Ayrton Senna’s 41 victories.
It was Lewis Hamilton’s second victory at the Belgian race — his previous for McLaren in 2010.
Lewis Hamilton is the first driver since Michael Schumacher in 2001 to claim six consecutive pole positions.