With rain hammering Suzuka for much of the day, there was less track action than normal but it was George Russell who topped the time sheets with Mercedes team-mate Hamilton coming in second.
Russell was over 0.8 seconds faster than champion-elect Max Verstappen in third as the British pair timed their fast runs perfectly on a drying track.
Hamilton recently enjoyed a run of five consecutive podium finishes in a season where Mercedes do not have the pace of the front-runners.
He then retired in Belgium before fourth and fifth-placed finishes in Holland and Italy, coming home ninth in Singapore last weekend.
While there was little that could be taken from the performance of the cars in such inclement weather and changeable conditions, Hamilton is hopeful of retaining Friday's speed.
Asked what he is expecting from Saturday qualifying - which is forecast to be run in the dry - the seven-time world champion replied: "No clue.
"I really have no idea, if we get it dry I imagine the Ferraris and Red Bulls will be quick but I really, really have no idea.
"I hope that we are fast but that is a hope that continues to be the case each week."
While Hamilton may not have enjoyed his first day back racing in Japan since 2019, he was still pleased to take some lessons heading into the weekend.
"It has been pretty dull," he added.
"It was just grey and wet, we got through a bit of running but it is going to be dry for the rest of the weekend.
"It has been OK, it has been very chill. There is always things to be taken from it, some of the stuff with set-up, tyre wear, tyre temperatures and the balance that we are moving around.
"There is definitely things to take from it and data on downforce loads and what wing level everyone else is on.
"On the positive side we were able to switch our tyres on so we didn't look slow, which is good."