The two sides looked set for their second goalless draw in the group until Xherdan Shaqiri slipped a pass through the Cyprus defence and Seferovic nipped in to lift the ball over goalkeeper Antonis Georgallides.
The Swiss, attempting to qualify for their third successive World Cup, went four points clear of Albania in Group E, regarded as the easiest of the nine European groups.
With coach Ottmar Hitzfeld serving the second game of a two-match touchline ban and the Stade de Geneve barely two-thirds full, Switzerland predictably dominated the game but struggled to break down the massed Cypriot defence.
Josip Drmic had a shot cleared off the line by Angelis Charalampous and Mario Gavranovic headed against the post in the opening minutes in a promising start.
Valentin Stocker curled a shot wide from 25 metres, Drmic fired into the side-netting after cleverly beating his man and Shaqiri twice had shots blocked in further Swiss attacks.
The pressure continued after the break as Georgallides made a one-handed save from Gavranovic's shot on the turn, pushed over another raking drive from Stocker and tipped away a Seferovic header.
The keeper made another save four minutes from time, blocking Shaqiri's shot with his legs after a well-worked move, but was powerless as Seferovic dinked the ball over him in the last minute.
Switzerland, unbeaten after six games, have 14 points, with Albania on 10 and Iceland nine. Cyprus are bottom with four.