Ferrari were confident of winning pole, but Alonso will start 10th with teammate Massa third, behind McLaren's Hamilton and Button.
Prancing Horse has been left red-faced in Italy
MONZA // It was supposed to be so easy. Luca di Montezemolo, the charismatic Ferrari president, said never in his 39 years involved in Formula One had he been so certain his Italian racing team would start their home grand prix from pole position.
Fernando Alonso, the Spanish driver who leads the world championship and with whom the Prancing Horse's home hopes were pinned, had even suggested qualifying would be "easy".
He had, after all, finished yesterday's final practice session before qualifying just 0.001 seconds behind Lewis Hamilton and was safe in the knowledge his car was capable of speeds of up to half a second quicker when he had to push.
But then, in the space of 10 tense minutes at the end of qualifying, it all went wrong.
Di Montezemolo, one minute smiling and chatting amiably with Jean Todt, the FIA president, was next seen storming out of the Ferrari garage in a fit of anger.
Alonso had qualified down in 10th place after suffering a suspected broken rear anti-rollbar.
"It was impossible to drive," the two-time world champion said, after watching Lewis Hamilton and Jenson Button lockout the front row for McLaren-Mercedes.
Alonso's teammate Felipe Massa will start today's race third - his best qualifying performance of the season.
Di Montezemolo, having sufficiently regained his composure, later explained his frustration at the setback.
"Of course, I am extremely disappointed," the Italian said. "This was one of the easiest opportunities in my career - and my career started in 1973 - to get a pole position in Monza.
"Alonso was absolutely the quickest and the car is competitive. We have to be disappointed."
Alonso said he had "no doubts" he would have been fighting for pole had his car not failed him, adding that it should have been "an easy pole position".
"It's maybe 15 years that something like this has happened, but it has and there's no point in crying over it," he said.
"The problem will be fixed for [the race], but of course this result changes everything as far as the race is concerned.
"We had the chance to increase our lead over our closest rivals, but now, it's likely that at least some of them will make up ground on me."
Certainly, McLaren will be looking to capitalise on Alonso's misfortunes in this afternoon's 53-lap race.
The English marque have won the previous two rounds of the world championship in Hungary and Belgium and know this afternoon offers a perfect opportunity for both their drivers to close the gap on the Spaniard in the standings.
Hamilton, in finishing 0.123s ahead of his teammate, claimed his fourth pole of the season and a 23rd of his career, yet was not pleased with his performance.
"I think practice was a lot better for me," the 27 year old, who topped the time-sheets in the weekend's second and third free practice sessions, said.
"I had much, much better laps in practice, but I can't complain. Generally, I didn't think that lap was anywhere near good enough.
"Nonetheless, I'm happy and I'm really happy for the team because they've been doing a fantastic job."
Hamilton's relationship with his team has been cast in doubt following speculation he has signed a pre-contract agreement with Mercedes-GP to race for the German marque from next season.
The rumours have overshadowed the on track action so far this weekend, yet the Englishman dismisses the notion his mind may be elsewhere.
"I haven't had any distractions this weekend, so it's been quite positive," he said.
"The support from my family and friends, as always, has been incredible, so I've just been enjoying the weekend and it's been pretty smooth so far."
Massa's future has also been the subject of speculation following a poor series of results that date back almost two seasons and have seen him not finish on the podium since October 2010 when he was third in the Korean Grand Prix.
The Brazilian acknowledged that a strong showing at his team's home grand prix, in front of his team's onlooking president, could be crucial in his fight to retain his seat at the sport's most successful racing marque for the 2013 season.
"I am very happy with this qualifying, the best in a long time for me," Massa, said.
"I know how important it is. I will give everything to win and do a good race. Getting back on the podium, here in front of our fans, would be wonderful. It's my second home race and racing here is always a fantastic feeling."
Di Montezemolo added: "Felipe has a huge opportunity to win the race, which would be important for him, for us and for his future."
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