Hamilton added that he was "really happy" with his first pole at Suzuka, one of the most challenging tracks.
Vettel, who has won four times at Suzuka in the past, but never with Ferrari, now lines up second, thanks to his lap of 1.27.791.
"It's been a really good day, every lap was fantastic", Hamilton told former McLaren team mate Jenson Button, who interviewed him for TV immediately after the session.
"Obviously we're quick in qualifying but it got very close at the end with the VSC and the restart".
"With the downforce we now have, it's three seconds faster than before and it's just insane speeds that this vehicle is throwing us around inside", he said.
"I've had plenty of opportunities to get this pole and I thought "I'm going make sure I'm going make it stick today". His Mercedes team-mate Valtteri Bottas was second, but three-tenths down on Hamilton and will take a five-place grid penalty after taking a replacement gearbox.
Red BulldriverMax Verstappen, who overtook Hamilton easily early on to win the race in Malaysia, is sixth in the standings and will be looking to build on his momentum in Japan.
"Last weekend was a bit of a disaster but we still got pole, which was unusual".
It is also imperative for Vettel to beat Hamilton in Japan if he is to keep his hopes of a fifth world championship alive, being 34 points down with five races remaining this season.
"It has been a really hard weekend and obviously I went off this morning but the guys did a great job getting the vehicle back together".
Vettel recovered from last on the grid to finish fourth but still lost further ground, having crashed out at the first corner in the previous round in Singapore. So, come rain or shine, I think this will be fun, this weekend.
Vettel needs a victory in the Japanese Grand Prix, due to take place on Sunday, to stand any realistic chance of winning the drivers' championship. It has worked out better this time and my knowledge of the auto is better than it was before, which has enabled me to go out and do the job. "We thought we'd be stronger in the last race but we were way off but we still got pole and finished second".
Red Bull's Verstappen collided with two Ferraridrivers Kimi Räikkönen and Vettel at Marina Bay Street Circuit.