However, after a slight delay, the flag went up for offside and replays showed Thomas Meunier had been caught ahead of the English defence in the build up.
England were awarded a penalty of their own on 39 minutes when Jordan Henderson was brought down in the box by Meunier. A corner was whipped into the box and Meunier placed a hand on Henderson's shoulder who made the most of the contact.
Rashford, who on Friday was awarded an MBE, stepped up to take the penalty and buried it high into the left corner.
It took England until 65 minutes to find a lead with a deflected Mount shot. Kieran Trippier managed to keep the ball in play before Mount tried to curl a shot around the Belgium defence but a deflection off Toby Alderweireld saw the ball loop over Mignolet and into the net.
The result puts England top of Group E after three games on 7 points and means they have now won 20 of their last 21 competitive home games. Belgium are one point behind in second place after three games.
"It doesn't matter how they go in. I found myself with a bit of space in the box and only had one thing on my mind, to get the ball out of my body and shoot. A big deflection, but you'll take them," Mount told Sky Sports.
"They made it tough for us, we were hanging in there at half-time, we got back into it at 1-1, and we knew we could regroup then, talk about the things we could do better, and fix the problems we were having.
"We've got the mentality, we've got the work ethic to get better and better and that's the path we're on."