The reigning European champions went into their final Group B game in Lisbon knowing they had to win in order to overhaul the Swiss at the top of the standings.
Former Arsenal man Johan Djourou put through his own goal four minutes before the half-time break, before AC Milan striker Andre Silva added the second just before the hour mark to send the Portuguese through and consign Switzerland to the play-offs.
Southampton stopper, Soares, who played a big part in helping Portugal win Euro 2016, got the full 90 minutes under his belt and will return to St Mary's in buoyant mood ahead of Sunday's Premier League clash with Newcastle.
Virgil van Dijk will also be pushing to feature against the Magpies after he played the entire game for the Netherlands as they defeated Sweden 2-0 on Tuesday. However, that was not enough to secure a second-placed play-off place ahead of their opponents, with France topping Group A.