Nico Rosberg scored his third successive pole position as Mercedes locked out the front row for the second consecutive race.
Fastest in all three practice sessions, Rosberg followed that up when it mattered most by taking top spot on the grid ahead of tomorrow's Monaco Grand Prix.
For a split second it appeared as if Hamilton would beat his team-mate, only to be ousted from pole by 0.091secs by the German, who was also on pole in Bahrain and Spain.
From such a mighty position, and unlike in the last two races when Mercedes have gone backwards, Rosberg and Hamilton should now be in a position to go on to take the chequered flag given the difficulty in overtaking around the streets of the principality.
Behind the Mercedes duo is a second-row lock-out for Red Bull, with triple world champion Sebastian Vettel ahead of Mark Webber.
Lotus' Kimi Raikkonen, four points behind Vettel in the championship standings, starts fifth and is joined on the third row by Ferrari's Fernando Alonso.
McLaren's Sergio Perez managed to get the upper hand on team-mate Jenson Button as the pair line up seventh and ninth either side of Adrian Sutil in his Force India, with Toro Rosso's Jean-Eric Vergne 10th.
On the super-soft compound in Q2 as the track had dried following rain before the start of qualifying, the six to drop out were of no great surprise, spearheaded by Nico Hulkenberg in his Sauber who will start 11th.
The German is joined on the sixth row by Daniel Ricciardo for Toro Rosso, followed by Lotus' Romain Grosjean.
The team just managed to get the Frenchman back on track following his shunt at the end of final practice and carrying out repairs.
Although Grosjean comfortably made it out Q1, he was anything but that in Q2 and lines up 13th, with Williams pair Valtteri Bottas and Pastor Maldonado 14th and 16th.
Caterham and Giedo van der Garde caused a major coup by qualifying into the second session for the first time this season, with the Dutchman to sandwich the Williams duo in 15th.
With the track at its worst in the opening 20 minutes, the drivers spent the entire session on the intermediate tyres.
Given the rain had relented at the start, as the track was drying so the times tumbled, Q1 still produced a shock.
That fell on Paul Di Resta as he failed to make it into Q2, leaving the Scot to start from 17th, equalling the worst grid slot of his career going back to the Belgian GP of 2011.
Behind Di Resta will be Caterham's Charles Pic and Esteban Gutierrez in his Sauber, with Marussia's Max Chilton 20th and the last of those to set a time.
On the back row of the grid will be Jules Bianchi in his Marussia, the Frenchman suffering an engine failure earlier in the session, with Ferrari's Felipe Massa bringing up the rear.
Massa suffered a heavy shunt in final practice, smashing into a barrier as he attempted to turn into Ste Devote at the end of the start-finish straight.
The initial impact into the first barrier was considerable as the front-left of his Ferrari took the full force before the car slid around 100 metres into a TechPro barrier at the run-off area of Ste Devote itself.
Given the damage, the team faced a race against the clock in a bid to carry out the repairs, only to fall short in their quest.
Informed it is exactly 30 years since father Keke won this race, a smiling Rosberg said: "That's nice, but it doesn't change much.
"I'm just very happy to be starting first. It's great to take pole, especially in Monaco.
"But in Barcelona (Spanish Grand Prix a fortnight ago) we struggled a lot (with the tyres). I was still 70 seconds behind the race winner.
"We're improving step by step, but there are still a lot of question marks that remain.
"It (the tyres) are our weakness. We can make the best of it and we can always create a few surprises."
Despite again trailing behind Rosberg, Hamilton is happy to start from second as he said: "I've been struggling.
"This weekend has been really difficult for me, so I'm really happy I can be up here (in the top three)."
Vettel, meanwhile, blamed himself for failing to make the front row, missing out by 0.013secs to Hamilton and just over a tenth of a second to Rosberg for pole.
"It was very close," said Vettel.
"Mercedes has been quick all weekend. I don't want that to sound like an excuse but I had a tenth missing and if anyone is to blame its me.
"I'm quite happy it's not a Lotus or a Ferrari ahead, so third is a good result and I'm still in a position to win this race."