Buoyed by his maiden victory in China a fortnight ago, Antonelli delivered another composed performance as he secured top spot in Suzuka by 0.298 seconds.
Russell holds a four-point championship lead over Antonelli but the Briton was no match for the Italian teenager during a session in which he grumbled about the handling of his car.
Australia's Piastri, who is yet to start a race this season, took third for McLaren, one spot clear of Ferrari's Charles Leclerc.
World champion Lando Norris will start fifth with Lewis Hamilton sixth, and Max Verstappen a distant 11th.
Russell opened his season with victory in Australia but Antonelli laid down his own championship marker by winning from pole last time out in Shanghai.
At the previous round, Russell's bid for pole was derailed by technical gremlins after he broke down in Q3. However, here he was simply outgunned by Antonelli's pure pace.
"Let's go, man", said a jubilant Antonelli over the radio.
In Q1, Russell detected there was something amiss within his Mercedes machinery.
"Something doesn't feel right," said Russell over the radio. Later, he added: "I think we're missing something here. We can't be lacking this much pace. Look at everything."
But Russell could not get on terms with Antonelli as he landed his second pole in as many weeks.
"He did a great job again," said Russell of his 19-year-old teammate. "It was a really strange session. We were both very fast all weekend. I made some adjustments after practice this morning, and then at the beginning of qualifying, I was nowhere.
"So, we need to understand that because I am very lucky again to be second. The last two weekends it has gone wrong come qualifying, but the race is tomorrow and there's still a lot to play for."
Antonelli added: "I'm super happy with the session. It was a good one, it was a clean one. I felt very good in the car and every run I was improving and improving."
Over at Red Bull, Verstappen's traumatic start to the new campaign took another turbulent twist when he was knocked out of Q2.
The four-time world champion, who began the week by ejecting a journalist from his news conference, claimed there was "something wrong" with his "completely undriveable" Red Bull as he laboured to 11th.
Verstappen was beaten by Red Bull teammate Isack Hadjar as he failed to make it into Q3. Hadjar will line up eighth.
