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Mercedes felt McLaren's pace on one lap could put them in the fight for pole, but that was a view of which McLaren themselves were sceptical.
Although McLaren set the pace at the end of the day, Mercedes' expected superiority was underlined on the race-simulation runs late in the second session, with Antonelli leading the way from Russell.
Piastri was next fastest once traffic that slowed him in the middle of his run was taken out of the calculation but he was still 0.25secs on average slower than Antonelli and 0.5secs off Russell.
Mercedes believe the qualifying fight will be close, but senior figures at McLaren said they think the competitive picture is the same as in the first two races, with Mercedes out in front.
Both Ferrari drivers seemed to be struggling for grip, and not on the level of McLaren, let alone Mercedes.
Leclerc suffered some wobbles through the Esses and ran off track at Spoon Curve later on, while Hamilton complained he was "slow because I've got no confidence in the car".
Ferrari sporting director Diego Ioverno said: "The gap is more or less where we expected it to be, also quite in line with the first two races, especially in the short runs. We have to improve."
Norris' early problem was a hydraulics failure, which McLaren fixed after half an hour. He had also spent a lot of the first session doing aerodynamic testing and felt he had had "a pretty terrible start to the weekend".
He added: "I just lacked a lot of laps. Even P1, a lot of my running all the morning was just aero running and the few laps I did get were not representative.
"Around a track like this you want laps under your belt to give yourself confidence. I am two or three steps behind on set-up and no long running."
He was far from the only driver to have problems. Racing Bulls' Arvid Lindblad took no part in the second session because of a gearbox problem that required a new part, while Audi's Gabriel Bortoleto spent nearly three-quarters of the session in the garage with an unspecified technical problem.
Cadillac's Sergio Perez missed about half the session while the team repaired floor damage caused by a collision with Williams' Alex Albon in first practice.
Fernando Alonso had his first taste of Suzuka this year in the second session, after American reserve driver Jak Crawford drove in the first.
The veteran Spaniard, who arrived late in Japan following the birth of his first child, was 19th fastest, two places and 0.355secs ahead of team-mate Lance Stroll.
Honda F1 boss Koji Watanabe said he hoped Honda, which has been blighted by poor reliability and a lack of performance at the start of their works relationship with Aston Martin, said both aspects should be improved for the company's home race this weekend.
Watanabe said: "We are focused on how we can improve the situation of vibration, mainly damage to battery area, but also this time for Suzuka we have improved energy management situation for more driving performance."
