Match commander Mark Sheeran, of the Metropolitan Police, praised the 30,000 Scots fans who attended the 2-0 defeat and insisted there had been no untoward incidents inside the Emirates Stadium.
Neymar had claimed he was the subject of racist jeers during his outstanding two-goal performance, but Scotland fans have made it clear any booing was directed at perceived play-acting.
Flashpoint: The banana-throwing incident allegedly occurred around the time of Neymar's second goal
The controversy deepened because a banana was thrown on the pitch as the gifted 19-year-old celebrated his second-half penalty. However, although there was no segregation inside the ground, it was hurled from a section of the North Stand dominated byBrazil fans.
There have now been eye-witness reports via Twitter claiming that the piece of fruit was thrown by a celebrating Brazilian supporter. And it is understood the SFA are considering approaching Arsenal for any CCTV footage that might provide conclusive proof that Scottish fans were innocent.
Hampden bosses have already contactedthe Brazilian football federation and match organisers Kentaro to express the anger of the Tartan Army at Neymar's allegations, which havebeen reported around the world.
Hotshot: Neymar's two goals against Scotland have added to speculation he could be on the way to Chelsea
'The Scottish FA also refutes claims from Neymar that he was the victim of racist jeers,' said an SFA statement. 'There was no evidence of such instances but the Scotland supporters have confirmed they booed the player for perceived unsportingbehaviour during the match.
'The tens of thousands of Scotland fans who travelled to London were, in fact, commended for creating a carnival atmosphere not just inside the stadium but across the city throughout the weekend.
'The Scottish FA has contacted the Brazilian Football Federation and the match organisers, Kentaro, to inform them of our information and supporters' unhappiness at the unfounded accusations.
'Representatives of the supporters groups have expressed their disappointment at the accusations, but it isimportant that this unfortunate incident does not detract from what wasa hugely enjoyable experience for tens of thousands of fans.'
Floored: Neymar was jeered by the Tartan Army for going to ground after a Scott Brown challenge
Match commander Sheeran was effusive in his praise for the Scottish support. Neither the police nor the stadium safety officer received any reports of racism.
'The Scottish fans' behaviour was first class,' said Sheeran. 'There were no issues at all inside the stadium.'
Neymar, meanwhile, was keen to play down the alleged incidents last night and said he would not make any formal complaint.
Asked about the police and SFA both insisting there had been no racism from the Tartan Army, the Santos starsaid: 'We cannot prove if it was a Scottish person or not (who threw the banana). It's in the past. I will go back to Brazil and play my football. I have already forgotten about it.
'It was one isolated case that did not show a good attitude. I hope the guy who did it will think about it and not do it again.'
The forward did, however, reject the view of some Scottish fans that he deserved to be booed for hitting the turf too easily.
'The times I fell down, I got knocks one in the knee, one in the face,' he added. 'I did my job, so I have nothing to say to that.'
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