The reigning world champion had been comfortably fastest for much of Q2, but a fuel pressure issue at the start of Q3 meant he had to be wheeled back to the garage.
The Silver Arrows confirmed that Hamilton’s team mate Nico Rosberg was delayed by a similar issue, but while the German was still able to complete two runs as planned, Hamilton only got going in time to do one run, completing six laps in a single stint, with his fastest time - good enough for third overall - coming on his final tour.
"It was a difficult qualifying, I don't really know what to say," a downbeat Hamilton reflected. "It's not a great feeling right now.
"I'm just trying to keep myself together. We're getting further and further into the championship and having more and more problems. This is becoming a norm for me.
"The good thing is we did get out to set a lap, so it wasn't as bad as some other qualifying sessions have been. Pole was there for the taking I think, but nonetheless I will do my best to salvage what I can tomorrow."
Hamilton downplayed his chances of being able to pass both Rosberg and Daniel Ricciardo’s pole-sitting Red Bull in normal circumstances on track, despite the fact his only victory on the Monte Carlo streets came from third on the grid in 2008.
"It's a one-stop - these tyres are so hard that it will be an easy one-stop," he said of the strategy for the race. "So there's nothing you can do with strategy.
"You can't overtake here so unless there is a safety car or rain or something I don't know what will happen…"
The polesitter has won eight of the last 10 races in Monaco - aside from Hamilton in 2008, the only other upset came last year when Hamilton took pole but was denied victory by his now-infamous late pit stop.