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The Ferrari ace was reported to the stewards for not slowing sufficiently when the rain-hit opening practice was red-flagged after Charles Leclerc had brought gravel back on the circuit.
Valtteri Bottas held off Max Verstappen to take second almost 13 seconds behind Hamilton in a breathless 53-lap race at the fast-flowing Japanese circuit.
It was Hamilton's third win in Russia, his fifth in six races and the 70th of his career, confirming he has the momentum to clinch a fifth title triumph with five races remaining.
The sports car is expected to fetch between 55,000 pound and 75,000 pound when it goes on sale through Europe's premier auctioneers H&H Classics at the Imperial War Museum.
The supercar maker moved to a guidance range for adjusted core earnings of 1.8-2.0 billion euros by 2022, rather than the 2 billion figure set by late Ferrari boss Sergio Marchionne
Reflecting on his position in Ferrari, Leclerc hoped that the team would allow him to race German driver Sebastian Vettel.
A barrage of questions were expected to be directed at Raikkonen following the announcement of his switch to Sauber earlier this week.
Ferrari have had the faster car than the Mercedes of late but they have failed to come up with the consistency required to win titles.
Leclerc has had a promising start to his rookie season, finishing sixth at the Azerbaijan Grand Prix, with 16 points from 14 races.
Lewis Hamilton waited until the end of lap 28 to come in for fresh tires, handing the lead to Bottas who was ahead of a charging Raikkonen.
The defending world champion qualified third behind Kimi Raikkonen, who took pole with Formala One's record fastest lap, and title rival Sebastian Vettel, who is 17 points behind the Briton.
Vettel was out-qualified by Ferrari team-mate Kimi Raikkonen for only the third time this year, but the Finn was also not happy.
Sebastian Vettel clocked a best lap of one minute and 16.170 seconds to wind up narrowly ahead of Valtteri Bottas of Mercedes by 0.059 seconds.
As it was Ferrari did not win and with the Italian soccer team missing the World Cup, golf might just have a chance to thrust itself out of the shadows.
Ferrari’s recent performances have followed their introduction of a new engine at the Canadian Grand Prix in June while Mercedes delayed their new unit until the French Grand Prix.