Raikkonen was left annoyed after he led the early laps from pole but Vettel passed him by using a later pit stop.
A Ferrari spokesman said: "The drivers are free to race. There was no plan whatsoever to get Sebastian ahead."
Vettel said: "There was no plan of any team orders. I can understand Kimi is not happy. I would feel the same."
Vettel went into the race leading Mercedes driver Lewis Hamilton in the championship by six points and came out of it with a 25-point lead - a clear race victory - when the Briton could finish only seventh after starting 13th.
Raikkonen pitted five laps before Vettel and came out behind slower cars, which he had to pass. Meanwhile, on a clear track, Vettel began setting fastest times and by the time he stopped he had made up enough time to emerge in the lead.
Ferrari said that Raikkonen ran on a pre-planned strategy to stop around lap 34 and said that although they knew he would come out among slower cars, it was inevitable that would happen at some point.
Raikkonen said: "I was called in, and that's about it. It didn't work out very well for me, but apart from that, it doesn't matter, does it?
"That's as much as I can say about it right now. I got the bad end of the story today. It is still second place but obviously it doesn't count a lot in my book at least."
Asked whether he knew why Ferrari had called him in at that time, he said: "I have no idea. They have reasons for why they do what they do. It is not up to me."
He said he would be asking the team to explain the decisions to him.
"We are a team and if you don't believe what you have been told then it will get very complicated at some point," Raikkonen said.
"Today, as a team, we wanted one-two. It happened. As for myself, it could have been better but we have just finished the race and who knows?
"We'll talk about it and I guess there are some reasons for everything that happened. As a driver I can do what I want but it is not how we work as a team."
Vettel, widely believed to be Ferrari's contractual number one driver, was asked if he and the team had discussed whether they would try to use an opportunity to get him ahead of Raikkonen if one arose.
He replied: "Not really. We spoke about the race before. The lead car normally has priority.
"If I had the choice, going in the pits first is maybe what you like to do.
"It is one of the rare occasions when the overcut [stopping after a driver you are following] decides the position, but from the team point of view there was no plan of any team orders.
"Today it worked in my favour and I take it, but we are a team and I can see Kimi is not happy."

About 250 people have been allowed to travel from the south for three days of meetings at Mount Kumgang resort.
Another group attended reunions earlier this week.
For most of those attending it is the first time that they have had any contact in over 60 years.
Millions of people ended up separated from loved ones by the physical division of the Korean peninsula.
The reunions taking place this week are only the second round in the past five years.
One of those travelling to the resort was the mother of a man who South Korea said was abducted by the North in 1972.
The South Koreans were chosen using a computerised lottery system from among thousands who applied.
Often accompanied by family members, they travelled in a convoy of buses from South Korea to meet their relatives.
Given their age and the infrequent nature of these reunions, they are unlikely to ever see each other again.

Klinger, 36, has hit three centuries in 10 Championship innings so far this season, averaging 94.83.
His side have five Division Two matches left in 2016, but he is likely to miss September's trip to Northamptonshire and the last game, the visit of Sussex.
"We have a baby due in mid-October," the Australian told BBC Radio Bristol.
"Once it gets within that four-week period, I can't be here in case the baby comes. I'd struggle to make it with a 24-hour flight back home if she went into labour. I'll leave on the 11th (of September)."
Sebastian Vettel and Ferrari denied they manipulated the Monaco Grand Prix to ensure the German beat team-mate Kimi Raikkonen.
[NEXT_CONCEPT]
A group of mainly elderly South Koreans have met relatives in the North, in the second of two organised reunions for family members separated by the 1950-53 Korean War.
[NEXT_CONCEPT]
Gloucestershire captain Michael Klinger is set to miss their final two County Championship matches of 2016 as his wife is expecting a baby in October.