Shortly after the Scottish tennis ace dispatched Novak Djokovic in straight sets Salmond unfurled a Saltire and waved it behind David Cameron's head.
Salmond is pushing the case for Scottish independence ahead of a referendum on Thursday 18 September, 2014.
Unfortunately for Salmond the stunt appeared to contravene tight All England Club regulations.
Its website states that "large flags (over 2ft by 2ft), banners, rattles, klaxons or oversized hats" are among prohibited items at the club.
As well as potentially landing him in hot water with the authorities, the flag-waving was criticised as a "stunt" by some political rivals ahead of next year's referendum on Scottish independence.
Shadow Scotland Office minister Willie Bain posted on Twitter: "In my experience, real tennis fans support their favourite players for who they are and how they play - let's keep the stunts out of it."
Liberal Democrat chief whip Alistair Carmichael penned a memo to the tournament organisers, saying: "Thank you for looking after the FM today. Next year, can you please search him more carefully?"
He added the hashtag #cringe.
A spokeswoman for the first minister said: "Scotland feels enormous pride that a young man from Dunblane has won Wimbledon.
"With flags of all kinds flying around Wimbledon, and even a Saltire above Downing St, one extra Saltire among a sea of flags seems like a fair way to celebrate."
Number 10 flew the Scottish flag today to mark Murray's appearance in the final.