Right back Stephan Lichtsteiner broke the deadlock with a looping header in the 78th minute and Xherdan Shaqiri, who sat out the first hour, added the second five minutes later.
Until then, the Swiss had carved out precious few chances against the South Americans who came without top players such as Bundesliga-based Claudio Pizarro, Jefferson Farfan and Carlos Zambrano.
Ricardo Rodriguez was Switzerland's most lively player in the first half and the left back's pile-driver free kick was parried from under the bar by goalkeeper George Forsyth.
Peru, who last qualified for the World Cup in 1982, were confident in possession but only threatened once in the first half when Paolo Hurtado's side-footed shot was tipped past the post by Diego Benaglio.
There was little change in the second half as the Swiss continued to labour while a noisy continent of around 1,000 Peruvian fans, armed with bicycle horns and drums, made more noise than the 14,000 home supporters.
However, the hosts finally broke through when Rodriguez crossed from the left and Lichtsteiner headed into the top corner. Six minutes later, a long ball was floated over the Peru defence to Shaqiri and he scored with a shot that went through Forsyth's legs.
(Reporting By Brian Homewood; editing by Martyn Herman)
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