Botes, who was born in Worcester in the Western Cape, played 35 times for Griquas in the Currie Cup before going to Italy in 2008. The 29-year-old, who plays for Benetton Treviso, has notched up 13 caps for the Azzurri since he was called up to the Italian Six Nations squad in January 2012.
"We cannot select our team on the basis that it's a nice story and it would be great for Tobias Botes to play for his country of birth in front of his home crowd. We decided to select the team we felt would be the most effective on the day," Brunel said at the team hotel on Durban's North Beach on Thursday.
Brunel also surprised by omitting experienced Leicester Tigers tighthead prop Martin Castrogiovanni from the starting line-up. The 95-cap strongman will start on the bench on Saturday.
"Castrogiovanni is on the bench because he had a long season and also played in the Aviva Premiership final with Leicester Tigers. He didn't assemble with Italy at the training camp.
"He joined the side here in South Africa from Hong Kong, whereas we have worked with Lorenzo Cittadini right from the start. It's a decision we took early and that is why Lorenzo is lining up against the Springboks on Saturday," he explained.
Brunel made seven changes from the starting XV which defeated Ireland on 16 March in the last round of the Six Nations tournament.
The 33-year-old flyhalf Alberto Di Bernado will make his international debut. Eighthman Serio Parisse leads the team for the 49th time in his career, while former captain Marco Bortolami comes back after missing the Six Nations due to injury.
"Marco is certainly one of the most experienced players we have at international level. He is a key man in our lineout strategy. During the last Six Nations tournament we played pretty well in the lineouts even without him, but it's great to have him back in our side," he said about the 94-cap veteran.
Brunel says his side is keen to test themselves against the formidable Boks and he is sure they will be physically up for the challenge.
"We are not worried about playing one
of the best teams in the world. We just have to match them physically. We know
where we are and if we want to improve like we did over the last couple of
seasons we have to continue playing the best in the world," he added.