In France, Vettel was handed a five seconds penalty and On Sunday, Raikkonen took a 10-seconds penalty, but Mercedes felt these punishments were not sufficient.
But the headlines belong to Vettel, who suffered a neck injury during practice on Saturday and was forced to wear supportive tape during the race, but came through for his fourth win of the season.
Opting to keep both cars out while the Ferraris pitted, it lifted them up to first and third with Vettel emerging just behind Bottas.
In a race with two late safety vehicle periods, reigning champion Hamilton went from pole position to the rear of the field before finishing second for Mercedes in a superb fightback.
Lewis Hamilton has promised he will "not give up" in what he describes as the "most intense battle we've probably all had" after the disappointment of not winning his home British Grand Prix. But then after the second Safety Car, initially it was fine, but he started getting really close and I had to push every lap like a qualifying lap. It nevertheless marked an impressive drive from the 2007 world champion following his earlier penalty.
"My team did an awesome job this weekend", said Hamilton, when he was, eventually, interviewed on the podium and after the two Ferrari men had departed.
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But Wolff's counterpart at Ferrari, Arrivabene, was livid.
Vettel finished 2.264 seconds ahead of Hamilton.
However, questions will again be asked about Mercedes' tactics after deciding not to pit to replace the tires. But with 20 seconds still separating the title contenders, it appeared Mercedes' best hopes of victory lay with Bottas in second, who had whittled the gap down to just two seconds at the front of the pack. "And in a flawless world, I would have had new tires - but it wasn't that kind of day for me", Hamilton said.
Bottas did well to hold off Daniel Ricciardo for fourth as the Finn's tires dropped off dramatically, while Verstappen retired in the closing stages with gearbox issues.
Pierre Gasly claimed the final point in 10th for Toro Rosso and Honda.
"This is the greatest race of the year and this is the greatest crowd and I'm sorry I couldn't bring it home for you today", Hamilton told his disappointed fans. "I gave everything I could, I was struggling to stand".
"I came here to clarify, if he actually said something like that", said Arrivabene, speaking to Sky Italia about Allison, who left Ferrari in mid-2016 and joined Mercedes in 2017.