Russell and Hamilton finished seventh and ninth respectively, reversing their qualifying positions, after a poor qualifying session and troublesome first stint on the hard tyres prevented them from fighting further ahead.
On the restart after a lap one red flag, Mercedes decided to put both of its drivers on new hard tyres to attempt a bold one-stop strategy on the demanding Suzuka circuit.
But its poor pace, particularly over the second half of the stint, ensured that it soon had to bail out of that plan and convert to a two-stopper, with both Hamilton and Russell bolting on mediums for the final third of the race as they were unable to move up.
Explaining why Mercedes went for the one-stop, which among the frontrunners was only achieved by Ferrari's Charles Leclerc, the team said it was trying to do something different than the cars ahead.
The fact that it had two sets of fresh hard tyres available, and effectively had already done its required lap on a different compound by starting on mediums, made a one-stop look more achievable and enticing than trying to do it on medium-hard.
"Principally, we thought that would be a way to be a bit different," Mercedes trackside engineering director Andrew Shovlin explained.
"The teams in the top ten that had two hards, that was us and McLaren. Red Bull and Ferrari
had two of the mediums and at that point there wasn't really enough information to
know how that hard and medium were going to compare.
"It would certainly be an easier way of achieving a one-stop with two hards than with a medium and a hard and because of that red flag we'd already run the medium.
"Then looking further down the grid there wasn't really any threat from the other teams. They were slower than us and not likely to interact, so really it was about offsetting."
But while Leclerc pulled off his one-stopper to climb from eighth to fourth, both Russell and Hamilton struggled for pace as their first hard stint went on, with Hamilton's woes compounded by picking up some damage at the restart that affected his car balance.
"The issue was that the end of our hard stint wasn't good enough. We were dropping off. We lost a fair bit of time in traffic but fundamentally we weren't quick enough and we're just trying to understand that now," Shovlin explained.
"The tyres in Suzuka run quite hot. There's a bit of overheating and when you get some traffic it just drops the grip, causes a bit more sliding and specifically we were struggling with the slower corners.
"There's a hairpin, the slow chicane as well. That was where we were losing a fair chunk of that time. It was difficult to get the car turned and it was just costing us a bit in both of those corners. And then obviously as the tyres are just getting older the sliding goes up and the temperatures get a bit higher and that was just compounding it."
Mercedes is still searching for answers as to why its first stint went so wrong, as its second stint on the hard and its final run on mediums proved much more competitive and more in line with what Ferrari and McLaren were doing.
"I wouldn't say we've got a complete understanding of that issue now. It's obviously very soon after the race," added Shovlin.
"That's one of the jobs that we're going to be getting into in the next few days trying to work out exactly what happened and why we dropped off so much more than for instance Leclerc, who did a very good first stint that was a lot longer."
