Rossi had started last, a penalty resulting from the previous round in Malaysia where he allegedly kicked out at Marquez on track with the outgoing champion crashing, but finished fourth.
The Italian would have been champion if Marquez and Honda team mate Dani Pedrosa had managed to beat Lorenzo but they finished second and third -- with Rossi decrying an "embarrassing" afternoon for the sport.
"This is not the atmosphere we wanted to experience at the end of an unforgettable championship," said Honda Racing Corporation vice-president Shuhei Nakamoto in a statement.
"We understand that its been a very difficult day for Valentino ... However, on the other side we cannot accept the strong accusations he has directed against our rider and Honda in the past weeks and in today's post race press conference."
Rossi had previously made accusations against Marquez in Australia of assisting Lorenzo, with the season finale overshadowed by controversy that officials had warned was poisoning the atmosphere.
Nakamoto said there was no evidence to support the claims.
"Today Valentino has alleged that Marc never attempted to pass Jorge, who has clearly had a very good pace all weekend which he demonstrated by taking a strong pole position in qualifying," he added.
"Marc was struggling to stay behind him during the race and both him and Dani have done a great job to not lose too much distance to Jorge.
Nakamoto said Marquez had planned to attack Lorenzo on the last lap but a late move by Pedrosa thwarted that.
"We are sorry that Valentino doesn't believe this is the case, but we are certain both Marc and Dani were pushing 100 percent to achieve the best result for the Repsol Honda Team and all our partners as always," he said.
"We cannot accept that these accusations continue to surface time after time, as this is the perception of one person -- which we respect -- but it is not the reality.
"Valentino is a great champion and clearly an intelligent individual so we truly hope that in time, once the dust settles, he can reevaluate what has happened and accept this was another great race from a wonderful season," he added.
(Reporting by Alan Baldwin, editing by Greg Stutchbury)
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