Hamilton will start 12th at Monza, with the 28-year-old failing to make it into the top-10 shootout for the first time in 67 races, stretching back to the 2010 Malaysian Grand Prix, so ending his run of four consecutive poles.
During the second session, Hamilton made a mistake at the Ascari chicane, running over a kerb and breaking the floor of his Mercedes, which was unknown to either him and the team at the time.
That resulted in Hamilton running wide at the sweeping right-hander of the Parabolica that soon followed, exacerbating the problem.
Come his second run, and with the clock ticking, Hamilton was impeded by Adrian Sutil in his Force India, earning his former friend a three -place grid penalty following a stewards' investigation.
In the immediate aftermath, and with championship leader Sebastian Vettel comfortably spearheading an all-Red Bull front row with his 40th career pole, an angry Hamilton said: "I drove like an idiot.
"That's the worst I've driven for a long, long time."
Hamilton's mood had softened once his ire had eased, but he remained critical of himself over two hours after the event.
"I still feel like I didn't do a spectacular job," said Hamilton.
"I did have damage to my car, and the engineers said I lost quite a lot of downforce, which would explain a lack of pace, but that was due to the mistake I made earlier in the session.
"Someone mentioned to me that it was the first time in 67 races I had not qualified for Q3, so I guess I can be a little easy on myself.
"But I just want to achieve my best for the team. They're working so hard, and all of us want to do as good a job as possible.
"Sometimes when you have those moments you just feel like you've let people down.
"But tomorrow is when you get the points, and I'll do everything I can to get them."
Team principal Ross Brawn believes Hamilton was being too hard on himself, but applauded the Briton for his attitude.
"We've got to know Lewis, and he is often his own hardest critic," assessed Brawn.
"It's quite endearing for a driver, of Lewis' level, to be willing to make that sort of statement.
"It's not what we are looking for him to do, but he felt he wanted to do that.
"You have to remember those guys are out there hanging it on the line, and things happen sometimes."
Brawn feels the team can also look at itself, especially for pitching Hamilton back into traffic as he missed out on a top-10 place by two tenths of a second, potentially lost behind Sutil, irrespective of the floor damage.
"We didn't get the best traffic, the clearest track, so we have to look at how we can operate as a team more effectively, and Lewis is part of that team," added Brawn.
"What no-one can accept is someone not trying their hardest, and we can't criticise either of our drivers for not trying their hardest.
"When these things happen it's frustrating, but if you look at his record this year it's the first mistake of any consequence he has made all year, which is a pretty decent record."
On what was a woeful day for Mercedes, Nico Rosberg will start sixth after a hydraulic issue restricted him to just five laps in final practice, later compromising his qualifying.
Behind the Red Bulls in a shock third place on the grid is Sauber's Nico Hulkenberg, remarkably the fastest Ferrari-powered driver as Felipe Massa and Fernando Alonso line up fourth and fifth.
Alonso, who seemingly criticised his team following the Hungarian GP and which earned him a rebuke from president Luca Di Montezemolo, is in the spotlight again for more contentious remarks.
Over the team radio Alonso is understood to have said "You're really idiots", after Ferrari's strategy failed to pay off.
With Lotus' Kimi Raikkonen starting 11th, it means Vettel's three title rivals are comfortably behind the German on the grid.
Jenson Button starts ninth in his McLaren, with Paul Di Resta now 15th given Force India team-mate Sutil's penalty, with Marussia's Max Chilton 22nd and last for the third time this year.