Conrad Jantjes and Danie Rossouw also crossed for South Africa, with Wales getting a late try from Ceri Sweeney. Montgomery was shown a second yellow card and sent off with 10 minutes remaining for a high tackle on Shane Williams.
"We should really have finished a lot better," South Africa captain John Smit said. "But we're happy with the result. To lose someone as substantial as Percy is hard but the boys played well."
In Toulouse, France, Les Tricolores ran in a total of five tries, with Thomas Lievremont, Aurelien Rougerie and Yannick Jauzion also touching down. Scrumhalf Dimitri Yachvili kicked four penalties.
"It was a very hard match for us physically," said France's Thomas Castaignede. "We were not at our best, but we will have to be next week."
France, which beat Canada 50-6 last weekend, hosts South Africa at Stade de France next Saturday.
In Genoa, Italy, two second-half tries within three minutes by Bernardo Stortoni and Federico Martin Aramburu lifted Argentina to a 39-22 victory over Italy. The Azzurri, who had edged the Pumas 30-29 in Cordoba last June, tied the score 22-22 in the 54th minute.
Gonzalo Tiesi and Francisco Contemponi also crossed for the Pumas. Felipe Contepomi had two conversions and five penalties.
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