The safety car was deployed immediately after the collision into the first corner that also led to the retirements of Sauber's Mexican Sergio Perez and Lotus's French driver Romain Grosjean.
Television replays indicated that Grosjean, whose car flew through the air over the nose of the Ferrari which also lifted off the ground, had triggered the crash by cutting across into Hamilton who had nowhere to go. Debris from the cars littered the track.
Grosjean said he wants to wait until he has seen television footage of the start of the Belgian Grand Prix before he judges who was to blame for the first corner crash, though inital impressions clearly suggested that he was at fault.
"(I had) a very good start and then boom - it was the end of the race. I haven't seen the images and I need to see them to have any point of view," he said.
"But the main thing is that everybody is OK. That is the most important for me."
Hamilton stormed over to Grosjean immediately after the accident and gestured at him in a manner that suggested he believed the Lotus driver was to blame.
Alonso's retirement was his first of the season, but whatever the result of the Belgian GP he will still leave the race as the points leader.
Perez said he was an innocent victim of the accident, which also left his front-row-starting team-mate Kamui Kobayashi with damage.
"It was on the braking for Turn 1 and then suddenly I had a big hit from other drivers and there was nothing I could do," said the Mexican. "We basically paid for a mistake from one driver."
Alonso had been set to equal Michael Schumacher's Formula One record of 24 successive points scoring finishes and has a 40 points lead over Red Bull's Mark Webber in the championship with eight races remaining after Spa.
The Spaniard, who could consider himself fortunate not to have been struck on the head by the Lotus, was slow to get out of the car but seemed unhurt.
Hamilton had been in trouble with McLaren even before crashing out of the Belgian Grand Prix after he sent his 997,000 followers sensitive telemetry details from his McLaren car in qualifying.
The British driver Tweeted sensitive telemetry information from qualifying, and while the Tweet later disappeared - as did a flurry of other messages he posted on Saturday explaining his poor qualifying performance in colourful terms - McLaren were not amused.
"Could you also tweet the race strategy and set up sheet. Thanks mate," joked former McLaren driver Alex Wurz, now working with rivals Williams as a driver coach, in a reply to Hamilton on the social network site.
McLaren chief Martin Whitmarsh confirmed on Sunday that the team had told Hamilton to remove the Tweet containing the telemetry - though needless to say the image has already been duplicated across the world, and indeed is on this very page.
Hamilton's message had intended to show his followers the difference in qualifying speed between his car and that of team mate Jenson Button, who started on pole position for the first time in three years.
Button qualified with a new specification wing while Hamilton's side of the garage stuck with the old one and paid the price on Saturday.
The 2008 champion, fourth in the standings but 47 points adrift of Ferrari's leader Fernando Alonso, qualified in seventh place.
Formula One teams are notoriously sensitive about the release of data from their cars before a race for fear rivals could gain an advantage from it, with the telemetry potentially also revealing key details about ride height.
Hamilton's Twitter problems, with some of his Saturday Tweets including acronyms based on obscenities, remained a paddock talking point on Sunday with British newspapers also reporting the details.
The 2008 world champion, whose contract at McLaren expires at the end of 2012 although he looks set to stay, also had his defenders, however.
"Lewis is a great example and an ambassador of taking motorsport into areas where probably people wouldn't have been particularly interested because he's young, and because he's black and because he's cool and because he's got friends who are similarly cool," said Mercedes GP chief executive Nick Fry.
"Formula One is really cool, it's a really interesting thing and there's lots of different aspects to the interest. More power to Lewis by communicating to people who previously would have had no interest."