Pathan was found guilty of violating the rules of fair play after making a mocking gesture towards Australian batsman Damien Martyn following his dismissal in Sunday's second one-day international triangular series final.
Pathan, 19, was reported under the International Cricket Council's strict rules on player behaviour by the two field umpires Rudi Koertzen and Daryl Harper as well as the third umpire Simon Taufel.
He was ordered to attend a hearing at the end of play and match referee Clive Lloyd issued a statement on Monday saying the paceman had been reprimanded for a level one breach.
"It's important that players and team officials at all times conduct themselves within the spirit of the game," Lloyd said.
In a spiteful finish to the series, Indian captain Sourav Ganguly complained to Australian skipper Ricky Ponting that he had been sledged by one of the Australians as he came out to bat.
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"I don't want to make public. It happened from the time I walked out of the gate until I reached the stumps," Ganguly told reporters.
"I'm not upset. I just told him (Ponting) I don't want to start it all over again. I told him I don't want to blow it out of proportion."
Ponting also refused to elaborate on Ganguly's complaint but confirmed the Indian skipper had spoken with him.
"He actually mentioned to me that one of our players had said something to him as he was coming out onto the field," Ponting said.
India arrived in Australia at the end of November and drew the four-match Test series 1-1 before taking part in the triangular competition which also included Zimbabwe.