At the restart after the first-lap red flag caused by the crash between Alex Albon and Daniel Ricciardo, Mercedes swapped George Russell and Lewis Hamilton from medium tyres to the hard compound in a strategy switch that targeted a one-stop plan.
But both drivers struggled for pace on the hards and, after failing to find sufficient gains after their first stop to another set of hard tyres, Russell and Hamilton reverted to a two-stop strategy to end the race on the mediums they used for the first lap.
Russell finished seventh, getting by Oscar Piastri late on, while Hamilton could only manage ninth in the Suzuka race.
Wolff blamed the poor pace in the first stint and said Mercedes will examine what caused it having been hopeful of fighting for the podium beforehand.
"We ended up where we started and it was just very difficult," Wolff told Sky Sports F1. "We had a second and third stint that was super quick and we would've been racing for a podium but an atrocious first stint.
"We need to find out what it was, was it too hot, were we overmanaging."
Wolff backed the one-stop strategy change by Mercedes during the red flag but was alarmed by the pace drop which forced it to change its plan.
"I think it was the right thing to do at the beginning because it looked pretty stable in terms of lap times," he said.
"They were not pulling away too much, the direct competitors, but then it suddenly dropped like two seconds a lap and two and a half second per lap. In that moment it was clear it wouldn't last."
Hamilton suspected even with a different strategy Mercedes would have suffered because it still needed to run two hard tyre stints across the race due to its pre-race selections.
Mercedes and McLaren opted for two sets of fresh hards and one set of fresh mediums for each of their drivers for the Japanese GP, while Red Bull and Ferrari both had one set of hards and two sets of mediums for each of their drivers.
"I don't know what the different strategy would've been, whether we stayed on the medium to start, but we still had two really terrible hard tyres to run through," Hamilton said.
"A real challenge today. I think I picked up a bit of damage at the beginning when Charles came around the outside and had huge understeer for the first stint and I couldn't turn the car through any of the corners, so that is why I let George go by.
"The hard tyre was pretty bad, as I said, but the medium tyre was better. In hindsight, it looks like we should have had two medium tyres. But in general, the car was pretty bad today."
