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.