His interjection came after David Cameron, responding to England's qualification for the 2014 tournament, congratulated the team and expressed "commiserations to the other home nations, including Scotland, who had an impressive win over Croatia last night".
To what sounded like gasps of shock from a number of his own backbenchers the Prime Minister then said: "But I'm sure now that everyone in the United Kingdom will swing behind the English team."
As some MPs cheered and others laughed, the Prime Minister added: "You can always dream and hope."
Later, Mr Salmond was asked after a meeting with Mr Cameron and other government ministers in Downing Street, if he would adhere to the PM's request and encourage Scots to support England.
As a smile crossed the FM's face, he told reporters: "I'm delighted that England have qualified for the World Cup; I congratulate them on their success. No doubt I'll find myself in the position in many of the games of giving England lots of support.
"If I remember correctly it was a previous First Minister (Jack McConnell), not me, who wanted to support any team against England."
But he then noted: "I doubt very much that you'll find me wearing an England shirt at any point during the World Cup."
When it was suggested he might be praying for England to lift the World Cup as a boost to the pro-independence campaign, Mr Salmond quipped: "You should know this Machiavellian reputation that through more than 20 years you have tried to impose upon me is totally unjustified."
Ahead of the 2006 World Cup, Mr McConnell caused controversy when he said he would be backing underdogs Trinidad and Tobago, who were in England's group, during the tournament.