The Mercedes pair went out for one final qualifying lap with less than a minute remaining and Rosberg lost control coming out of the Mirabeau turn, sliding down an escape road. After Rosberg backed out onto the circuit, a yellow flag came up which meant that Hamilton could not improve on his time.
''I thought it was over once that happened, because I thought the track could ramp up and somebody else could beat the time,'' Rosberg said. ''Of course that's not great, but that's the way it is.''
Stewards later said they are investigating Rosberg's maneuver on turn 5.
''I just locked up, the outside front (tire), I think it was, or the inside, I'm not sure,'' Rosberg said. ''I was still trying to make it but in the last moment I had to turn out because I was going to hit the tire wall, but I managed to go into the escape road.''
It's the second pole of the season for Rosberg. Hamilton has the other four.
Rosberg's leading time was 1 minute, 15.989 seconds, with Hamilton clocking 1:16.048 and Ricciardo timed at 1:16.384.
Hamilton has won the past four races and leads the overall standings by three points from Rosberg, who won the season opener in Australia, where Hamilton retired with engine failure.
Four-time defending champion Sebastian Vettel of Germany finished fourth, while Fernando Alonso of Ferrari was fifth.
While Rosberg was smiling at the post-qualifying news conference, Hamilton looked stern-faced and gave short answers. He would only say ''not really much'' and ''I was on target, yeah'' when asked what he thought about the incident.
Rosberg tried to soothe the situation.
''Of course I'm sorry for Lewis, I didn't know where he was,'' Rosberg said. ''Of course, yeah it's not great.''
Asked to respond to Rosberg's apology, Hamilton shrugged his shoulders and mumbled: ''I don't have an answer to it.''
Told that it was ironic that Rosberg's mistake had led to the yellow flag and stopped the British driver, Hamilton flatly responded ''yeah, it's ironic.''
On the track, Rosberg looked jubilant - as if he had proved a point - clenching his fists victoriously as he stepped out of his Mercedes, with Hamilton standing close by.
Hamilton, the 2008 F1 champion, recently questioned his teammate's hunger to win at the highest level and referred to what he considered Rosberg's easier upbringing.
''I come from a not-great place in Stevenage and lived on a couch in my dad's apartment, and Nico grew up in Monaco with jets and hotels and boats and all these kind of things,'' Hamilton said Thursday. ''If I were to come here believing that Nico is hungrier than me then I might as well go home.''
Given that nine out of the past 10 Monaco GP's have all been won from pole position, Rosberg has a great chance to reclaim the lead from Hamilton if the stewards don't punish him. Rosberg won from pole position here last year for his maiden win.
Ricciardo again outperformed Vettel in qualifying, and has now qualified higher than him in four from six races.
''It's nice to fight at the front of the field,'' the Australian said, although he felt the times could have been better.
''I think all three of us don't seem to be too pleased with ourselves,'' he said. ''I think we all feel that we've left something on the table.''
Daniil Kvyat lost control of his Toro Rosso coming of the tunnel section in Q1, with the front wing making contact with the barriers and ripping off part of the nose. The Russian driver was able to continue after a brief visit to the pits.
In Q1, Marcus Ericsson tried to pass Felipe Massa inside the Mirabeau turn, but nudged his Caterham into the side of Massa's Williams, sending both into the barriers.
Hamilton was fastest in Q2 ahead of Rosberg, Vettel and Alonso. Vettel seemed unhappy with the car's reliability, saying ''this needs to be sorted out'' over race radio.