Despite Leclerc winning from pole in Belgium and Italy, a third Saturday success on the spin was thought unlikely as Ferrari have struggled at high-downforce events this year.
But with an upgraded front wing and floor, Ferrari were right in the mix around Marina Bay and Leclerc snatched P1 by two seconds from Hamilton, with Sebastian Vettel missing out due to an error on his final Q3 run, having had provisional pole beforehand.
Max Verstappen had come into the weekend expected to rival Hamilton for dominance, but the Red Bull star was more than half a second adrift of Leclerc, compounding Wolff's confusion.
"This is a circuit we thought the Red Bulls and Mercedes would battle for pole," Wolff told Sky Sports.
"Their car is fast, they did a good job and we have to get our act together tomorrow.
"They are gaining a few tenths on the straights, but they are also very quick in the corners. It's just quicker everywhere."
The pole-sitter has won in all but three of the stagings of the Singapore GP, although Hamilton was victorious the last time Ferrari secured P1, as Vettel and Kimi Raikkonen crashed at Turn 1.
And Wolff was keen to stress how the race could change if his drivers can secure a strong launch.
"The statistics are against us but the race has not started," he said. "If Lewis is able to get a good start and Valtteri can get up a position then we're in a good position."
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