Hamilton's problems all began as a bad start allowed Vettel to easily get ahead with Bottas also squeezing up the inside into Abbey.
He fell to 16th but recovered to second, ahead of Raikkonen who completed the podium.
In their official ruling after reviewing video evidence, stewards said Hamiton "left significant room on the inside of Turn Three" and that Raikkonen "locked up his right front tyre, understeered and caused a collision".
He was slapped with a 10-second penalty and two points on his drivers' licence. Vettel pitted from the lead, but Bottas stayed out, to lead on lap 34, as did Hamilton.
Vettel made a cracking start from second place to beat Hamilton to the first corner.
Qualifying for Sunday's race takes place later Saturday.
"I deserved the penalty, I took the 10 seconds".
"We got so much support", he went on, adding in a waspish swipe at Ferrari: "Interesting tactics, I would say, from their side, but we'll do what we can to fight them". Hamilton finished second and surrendered more ground to the German in what is turning out to be an epic and see-sawing title fight.
Arrivabene says he was anxious about Vettel's pain, but then praised the German's commitment. "My view, I did the best that I could, but there seems to be opposite looks of what I'm doing unfortunately".
Toro Rosso driver Pierre Gasly was the only one of the dropzone contenders to find time on his second run, declaring himself happy he got the maximum out of the auto.
The appearance of the safety auto on the 33rd of 52 laps, after Sauber's Marcus Ericsson crashed, was greeted with a huge cheer from the 140,500 crowd and was just what Hamilton needed to close the gap.
Vettel has emerged the clear victor from F1's first-ever triple header of races having led Hamilton by a point going into the French GP on June 24. "I gave everything I could, I was struggling to stand".
"I can't really comment as I don't know the thought process that went on there, but I do know there was widespread criticism of the leniency of the penalty given in France". So I was nervous I had lost part of my floor or something because the vehicle was moving for unknown reasons, but then it started to get better and better, after some tweaks to the settings.