Alonso, 77 points adrift of the German with five races remaining, was sixth in a session that saw four teams fill the top eight places in pairs - with the Mercedes duo leading the two Red Bulls, then the Ferrari and Lotus pairings.
Hamilton's best time of one minute 34.157 seconds, on a gloriously sunny day at the Honda-owned circuit overlooked by its giant Ferris wheel, was set on the hard tyre and was 0.330 quicker than Nico Rosberg's.
The times compared to the fastest lap in last year's opening practice of 1:34.507.
Vettel, who is chasing his fifth win in a row and has been on pole position in the last three, was 0.611 off the 2008 champion's pace with Australian team-mate Mark Webber fourth.
Webber was using a new chassis after retiring at last weekend's Korean Grand Prix with his car in flames after being hit by Force India's Adrian Sutil.
Vettel has won three of the last four races at Suzuka, a favourite track where he won the 2011 title and can count on a large contingent of local fans.
Brazilian Felipe Massa, runner-up at Suzuka last year, was fifth fastest ahead of Alonso while Romain Grosjean went quicker than his Lotus team mate Kimi Raikkonen.
Australian Daniel Ricciardo, who replaces Webber at Red Bull in 2014, broke up the two-by-two sequence with a lap that sandwiched him between the two McLarens of Mexican Sergio Perez and Jenson Button.
The main incidents came from those well down the pecking order, with Venezuelan Pastor Maldonado parking up at the Spoon curve when his left rear wheel came off and bounced across the track.
Marussia's French driver Jules Bianchi, who has a fairly meaningless 10 place grid penalty for the race after collecting a third reprimand of the season in South Korea last weekend, and Caterham's Giedo van der Garde ended up in the tyre wall at Degner.