Zan Vipotnik gave Slovenia an early lead, but an own goal from Erik Janža and a strike from Dan Ndoye turned the match around before half-time.
The victory gave Murat Yakin’s side three wins from three matches in League B Group 1.
Vipotnik gives Slovenia early lead
Slovenia made a dream start, taking the lead after just two minutes.
Vipotnik controlled the ball after Switzerland failed to deal with a counter-attack before turning and firing a low shot beyond Gregor Kobel.
It was the first goal Switzerland had conceded in the Nations League campaign.
Janža own goal brings Switzerland level
Switzerland responded quickly and equalised in the 10th minute.
Remo Freuler’s effort took a decisive deflection off Slovenia defender Erik Janža, wrong-footing goalkeeper Jan Oblak and finding the back of the net.
The hosts continued to push forward after restoring parity, with Slovenia forced into a largely defensive approach.
Ndoye completes comeback
Switzerland completed the turnaround in the 38th minute through Dan Ndoye.
Freuler played the ball towards Zeki Amdouni, and after a scramble inside the Slovenia penalty area, the ball fell to Ndoye, who calmly found the bottom corner.
The goal gave Switzerland a 2–1 lead at half-time.
Switzerland hold on for third straight win
Slovenia pushed for an equaliser after the interval, but Switzerland remained the more dangerous side for long periods.
Oblak was forced into several important saves, including efforts from Freuler and Johan Manzambi, while substitute Winsley Boteli came close to scoring his first international goal late on.
Slovenia almost snatched an equaliser in the closing stages when substitute Žan Celar found himself in a promising position, but Kobel made the necessary save to preserve Switzerland’s lead.
Switzerland lead Group B1
The result moved Switzerland to nine points from three matches, giving them a five-point advantage over Slovenia and Scotland.
Switzerland had previously defeated North Macedonia 3–0 before recording another 3–0 victory away to Scotland.
• Switzerland: Erik Janža 10' (og), Dan Ndoye 38'
• Slovenia: Zan Vipotnik 2'
Switzerland will face North Macedonia again on Tuesday, 6 October, while Slovenia will look to respond in their next Nations League fixture.