The McLaren driver edged out Kimi Antonelli by 0.092 seconds in Suzuka on Friday, with George Russell third in the day's second practice session.
Lando Norris missed the first half of the one-hour session with a hydraulics leak and was fourth, half-a-second down on Piastri in the other McLaren.
Charles Leclerc finished fifth, a distant seven-tenths behind Piastri, and one place ahead of Ferrari teammate Lewis Hamilton. The seven-time world champion was 0.847 seconds off Piastri's pace.
Max Verstappen's torrid start to the new season looks set to extend into the third race after he finished only 10th.
Verstappen, a winner here last year, ended the one-hour running 1.3 seconds behind Piastri, with Isack Hadjar in the other Red Bull even further back in 15th.
In the first practice session on Friday, Russell edged out teammate Antonelli, followed by Norris and Piastri.
Mercedes have set the benchmark this season, with Russell and Antonelli on one victory apiece. Up until Friday, either Russell or Antonelli had also occupied the top spot in every practice session so far.Â
However, Piastri's speed later in the day will offer encouragement for constructors' champions McLaren and Norris, who has endured an underwhelming start to his title defence.
McLaren are also looking to bounce back from a horror show at the previous round in China where mechanical gremlins saw both Piastri and Norris fail to start the race.
Piastri is looking for his first race start of the season, after crashing on the way to the starting line in Melbourne, before the electrical problems harpooned his hopes in China.
Hamilton landed the first Ferrari podium of his career in Shanghai, but he appeared down on belief in practice at Suzuka.
"I am very slow because I have no confidence in the car," he said in the closing moments of the session.
After his strong showing in China, British driver Ollie Bearman, currently fifth in the standings, took ninth spot.
Audi's Nico Hulkenberg was seventh, one place clear of Williams' Alex Albon as Verstappen rounded out the top 10.
- with PA, AAP