Unlike in the previous grand prix at Singapore, Ferrari sought to redress the balance by putting Leclerc back in front, but squabbling over the team radio appeared to delay that happening, with Vettel seemingly reluctant to make way.
Looking at the situation from the outside, reigning champion and rival driver Lewis Hamilton said the dynamic at Ferrari was clearly changing in favour of Leclerc.
"It is an interesting dynamic because Seb was number one, and now he clearly isn't", said Hamilton.
Asked about the situation at Suzuka today, Leclerc admitted that "there were some misunderstandings from the vehicle, but we've had a discussion and everything is clear now. I think we can improve, though, so we see where we are on Sunday morning".
Leclerc, who started from pole position, agreed to give Vettel, who started third, a slipstream down to the first corner to ensure Ferrari led the race on the opening lap.
Hamilton admitted that it was just an "assumption", but urged Ferrari to find the right way to "manage" the pair and their "friction".
Hamilton heads into Sunday's storm-threatened Japanese Grand Prix needing to outscore Valtteri Bottas by a mere five points over the next two races - here at Suzuka and in Mexico in a fortnight's time - to secure his sixth world championship.
"And what's clear is that the scenario wasn't clear for each of the drivers, beginning the race, and I feel that is crucial".
"I do understand", said Hamilton. "I've not had a team back the other side so much, so heavily, before".
His teammate Charles Leclerc said separate meetings with Ferrari boss Mattia Binotto took place in the days after the Russian GP.
Asked whether his own experiences as a rookie alongside designated team leader Fernando Alonso at McLaren in 2007 meant he could relate to Vettel's current predicament, Hamilton said: "I mean - again, it's an assumption, because we're looking [at Ferrari] from the outside, so I don't know what's happening inside, I don't know what Seb's feeling, so it's hard to say I can relate to it". Both drivers went on to complete the race to claim the team's first one-two finish since July.
"There are drivers that always wanted that number one status".
"I think you can get that number one status weekend in, weekend out, rather than over the course of the season". I like to earn that.
"I think it's pretty clear if the typhoon is going to come here there's no way we can drive", said Leclerc.
"If you already know you're number two, it's kind of defeatist".