This was despite securing a sixth win of the qualifying campaign.
Two goals in as many minutes from defender Philippe Senderos teed up a comfortable 3-0 victory in Luxembourg to see Switzerland in pole position in Group Two, three points above second-placed Greece.
Arsenal centre-half Senderos netted in the sixth minute to put his side ahead, before repeating the feat two minutes later as the Swiss took control of both the match and their hopes of a place in South Africa.
Benjamin Huggel made it three after 22 minutes, and the hosts were unable to muster a response.
Greece could yet steal top spot from Switzerland, after Theofanis Gekas hit four goals in a 5-2 defeat of Latvia.
Gekas' opener after four minutes was cancelled out by two Maris Verpakovskis strikes.
But a Gekas penalty, after Giorgios Samaras was brought down, brought Greece level - and his third goal of the night put the hosts in front.
Celtic forward Samaras then scored with a clever overhead kick 17 minutes from time - and Gekas tapped in his fourth to complete the victory.
Greece require a win over Luxembourg in Athens on Wednesday to secure their play-off place - and a favourable result could see them qualify automatically, if Israel can win in Switzerland.
Israel recorded their fourth win of the campaign in the penultimate round of matches with a 3-1 defeat of Moldova to keep their play-off hopes alive.
Elyaniv Barda struck twice, either side of a David Ben Dayan goal, as Israel established a three-goal cushion at Ramat Gan national stadium before Denis Calincov's late consolation for the visitors.
Israel are two points behind Greece.