The Commons leader criticised the Scottish Nationalists for their speed in passing through the division lobbies after they forced five votes during the match.
Mrs Leadsom said it was “entirely in order” for the SNP to vote, but condemned them for “staggering” through the lobbies - preventing MPs, doorkeepers and other Commons staff from watching the game.
Votes on motions linked to public spending could only take place from 7pm - the kick-off time for England’s second round tie.
Five votes occurred, including one regarding devolution, and took approximately 66 minutes.
The SNP’s Commons leader Pete Wishart called for the implementation of electronic voting as he raised the issue after Mrs Leadsom delivered the Business Statement.
He said: “I understand some of my Conservative friends got just a wee bit upset on Tuesday evening for having to vote on an estimates process, and apparently just by doing their job it got in the way of being able to cheer on the national English football team.
“Well apparently it’s all the fault of us nasty Scot Nats for daring to vote in a parliamentary democracy, how dare we.
“But salvation is on its way and there is a solution available for my footy-fixated Tory friends: and that is just to stop wandering round and round aimlessly for 20 minutes in a head count in stuffed division lobbies, and try and introduce some modern voting facilities and come into the 21st century.”
Mrs Leadsom replied: “I think what I would observe is that the Scottish Nationalist Members of Parliament should certainly not be playing in the World Cup due to their slowness of the 33 of them through the lobby.
“They showed no ability to sprint, and whilst it is entirely in order for them to vote at all times as was pointed out on the day, nevertheless, for the Sergeant at Arms to have to go twice into the lobby to find out what was causing such a delay for 33 of them to stagger through didn’t only prevent those wanting to watch the football from this chamber, but it also prevented the doorkeepers, the many staff who support us.
“And it was just plain mean to do that.”