The two-legged play-off matches will be played on 14 and 18 November, with the draw to take place on Monday.
Switzerland's goalless draw with 10-man Israel was enough to send them through but Ottmar Hitzfeld's side were far from comfortable even after the visitors had Avihay Yadin sent off after 59 minutes.
"The team was nervous, you could see that. There were many errors and unnecessary fouls," Hitzfeld said.
"But the goal was to qualify and we made it - the goal is achieved.
"Compliments to the whole team and to each and every player. It's another success for me and a dream being fulfilled, it's a present that Switzerland has given me."
Also in Group Two, Greece made sure of their play-off place with a 2-1 win over Luxembourg, with Vassilis Torossidis and Theofanis Gekas putting the 2004 European champions ahead before a late own goal by Avraam Papadopoulos.
Slovakia triumphed on a snowy night in Chorzow to qualify for South Africa
The Greeks had needed at least a point to make the play-offs as Latvia beat Moldova 3-2.
"Luxembourg was a very difficult opponent and made things tough for us," Greece coach Otto Rehhagel said afterwards. "This was a very important game and we could have lost everything."
Like Switzerland, Slovakia also had a struggle to seal their progress, taking the lead in the third minute on a snowy night in Chorzow through Seweryn Gancarczyk's own goal and relying on some key stops from their goalkeeper Jan Mucha to hold on to their lead.
Slovenia beat San Marino 3-0 to finish behind the Slovaks in the same group and end Northern Ireland and the Czech Republic's slim hopes of making the play-offs.
Despite being without the injured Cristiano Ronaldo, Portugal easily sealed a play-off berth - thumping Malta 4-0 in Group One thanks to goals from Nani, Simao Sabrosa, Miguel Veloso and Edinho.
Compliments to the whole team. It's another success for me and a dream fulfilled
Switzerland coach Ottmar Hitzfeld on reaching the 2010 World Cup finals
Manchester United midfielder Nani calmed the home side's nerves by firing into the bottom corner from the edge of the area after 13 minutes and Simao hammered home a second goal before half-time.
Veloso's crisp finish made it 3-0 after Liedson failed to convert Nani's pass and Simao set up Edinho to wrap things up late on.
"For sure some points lost at home made life difficult for us but the important thing is that we made it and now we have to prepare for these two matches," said Portugal coach Carlos Queiroz.
Portugal's win rendered Sweden's 4-1 victory over Albania meaningless, and ensured Lars Lagerback's side - which includes Barcelona striker Zlatan Ibrahimovic - missed out on the play-offs in a group that was won by Denmark.
In Group Six, Ukraine made sure of second place behind England with a thumping 6-0 win in Andorra, a result which eliminated Croatia despite their 2-1 victory in Kazakhstan.
Andriy Shevchenko, Oleg Gusev, Yevgen Khacherdi, Yaroslav Rakitskyy, Yevgen Seleznov and Andriy Yarmolenko shared the goals for Ukraine in Andorra La Vella.
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