Haris Seferovic broke the deadlock early on, Blerim Dzemaili missed a penalty but later scored before the Swiss were awarded another spot kick, this time converted by Ricardo Rodriguez.
The Swiss have a maximum 24 points in Group B, three ahead of Portugal although they still have to visit the European champions for a showdown in Lisbon in their final game.
Portugal, who beat 10-man Hungary 1-0 away, have a vastly superior goal difference.
Seferovic opened the scored with an untidy effort in the ninth minute as he turned Stephan Lichtsteiner's cross towards goal and the ball bounced off the post and then goalkeeper Andris Vanins before trickling over the line.
Switzerland quickly won a penalty when Kaspars Gorkss brought down Admir Mehmedi but Dzemaili missed from the spot.
Dzemaili then squandered another good chance by side-footing wide from Mehmedi's cross but finally scored when he collected Seferovic's pass and rounded Vanins in the 55th minute.
Three minutes later, Mehmedi was felled by Aleksandrs Solovjovs and Rodriguez made no mistake with the penalty.
Dzemaili completed an eventful match by hitting the post.
(Writing by Brian Homewood in Berne; editing by Ken Ferris)
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