The 27-year-old was fastest throughout all three sessions around the Yas Marina circuit that was bathed in warm fading sunshine when the session began and was under the floodlights when it ended as darkness set in.
Hamilton finished a third of a second quicker than Red Bull's Mark Webber as team-mate and championship leader Sebastian Vettel could only manage third, the first time he has failed to make the front row of this event.
Vettel, whose car endured a brake issue in final practice that kept him consigned to the garage for all but two early installation laps and the final four minutes of the hour, rarely looked comfortable during qualifying.
Vettel, however, failed to make it back to the pits, pulling his car over on track at turn 18 after qualifying had concluded, which will be cause for the stewards to investigate.
After the middle 15-minute session neither Force India failed to make it into Q3 for the second straight race as Nico Hulkenberg qualified 11th and Paul di Resta 13th, the duo split by two tenths of a second.
A fading Michael Schumacher, heading into retirement for a second time at the end of the year, starts 14th for the second successive race in his Mercedes.
Behind Senna, at present, will be Sauber's Kamui Kobayashi and Toro Rossos of Daniel Ricciardo and Jean-Eric Vergne, the latter failing to make it out of Q1 for the eighth time in 18 races this season.
The Frenchman, who will enjoy a second season at Toro Rosso next year along with Ricciardo following confirmation of the drive on Thursday by the Faenza-based squad, spun late on his final flying lap to leave him 18th.
Vettel, who was ordered by engine suppliers Renault to stop the car, was unable to throw any light on the reason why.
The German's car has suffered two alternator failures in races this season, and if an engine change is required it will mean a 10-place grid penalty.
"I don't know why I had to stop, I was asked to stop," said Vettel.
"It's probably some problem, but it shouldn't be something major.
"It was not ideal this morning (with the brake issue), but we were settling in this afternoon and the pace was there.
"Overall I wasn't entirely happy with qualifying. I should have been quicker, but whether I had enough to beat Mark is on another sheet of paper."
With Vettel four places ahead of Alonso on the grid, he added: "We have seen so many up and down races this year.
"From where we start is quite good, we're close to the front and we go from there.
"Strategy wise we're still not 100% clear, but we have to look after ourselves, and race this guy (referring to Hamilton)."
As for Hamilton, he was unable to explain either where his speed had come from, even though this has long been one of his better tracks.
"I don't know," said Hamilton when asked.
"The car has been feeling fantastic, great from the get go, but we've no upgrade package so I don't know. It was just great."