The hosts continued to pile forward in the opening quarter of an hour, forcing a string of corners to keep San Marino on the defensive, but the visiting side kept clearing the ball.
Simoncini continued to be tested by the hosts as half time approached, but the San Marino keeper punched several corners clear while saving from a Ricardo Rodriguez effort, leaving the visitors just a goal down at the interval.
Fabian Schar briefly thought that he had doubled Switzerland's lead when he smashed the ball in from an Inler cross, but the referee ruled the finish out for an offside.
The hosts did add a second a couple of minutes later though as Davide Cesarini was penalised for a handball in the box, leaving Inler to score from the penalty spot.
Switzerland made it three just after the hour mark as Schar drilled another effort towards the goal, leaving Simoncini to punch it clear as far as Admir Mehmedi, who struck at the first time of asking to add to the score.
The hosts were awarded their second penalty of the night inside the final 20 minutes when Alessandro Della Valle tangled with Schar, leaving Johan Djourou to thump the ball down the middle for Switzerland's fourth.
Pajtim Kasami was on target to make it five just three minutes later, latching on to a ball forward from Francois Moubande before blasting it in from the edge of the penalty area.
Della Valle's desperate defending landed him in trouble again inside the final 10 minutes as he brought down Eren Derdiyok, allowing Embolo to become the third player to score from the penalty spot for the home side.
It got worse for San Marino before the full-time whistle as Derdiyok burst through again, heading the ball past Simoncini from a Renato Steffen cross.
With Slovenia being held to a draw with Lithuania, Switzerland are now guaranteed a second-place finish behind England in Pool E.