The gamble on the weather backfired and the unhappy Monegasque qualified 10th for Saturday's Sao Paulo sprint race after red flags and rain at Interlagos left him with no lap time on the board from the final phase.
"Am I the only one on inters?" Leclerc asked over the team radio during his first lap out of the pits when he realised everyone else was on soft slick tyres rather than the slower damp track option.
"There's no rain," he added.
The Ferrari driver was then forced to pit again but Mercedes' George Russell slid into the gravel and triggered red flags to halt the session.
The rain then came down more heavily, denying him the chance of a flying lap.
Leclerc, who is battling Red Bull's Sergio Perez for second place in a championship already won by Max Verstappen, will start alongside the Mexican on Saturday in a 100km race that determines Sunday's main grand prix grid.
Haas' Kevin Magnussen, the first out of the pitlane in Q3, took his maiden pole position.
"I will speak to the team and understand what we can do better in those conditions," Leclerc said.
Ferrari's season has been hit hard by errors on all sides and reliability issues.
Leclerc was leading his home race in Monaco from pole before a strategy error left him fourth.
At the Dutch Grand Prix, Ferrari had only three tyres ready for Carlos Sainz at a pitstop.
"What is going on in Ferrari and who is going to take charge of this situation because it has been going on all year?" 1996 world champion turned pundit Damon Hill said on Sky TV.
"You can see they have the potential and Charles is criticising the team on the radio effectively by saying 'nice one guys,' but he has to assume some responsibility as well," added the Briton.
"Maybe they aren't letting him do that or maybe he hasn't got the courage to assume it for himself."
