Valon Behrami, Fabian Schar and Stephan Lichtsteiner were all booked for fouls on Neymar, but Petkovic insists Switzerland did not set out to target the Paris Saint-Germain forward, who started his first game since February after recovering from a foot injury.
"No, most of the duels were perfectly clean and very often we had one-on-ones with Neymar," Petkovic told a news conference.
"One of the key ingredients [of the result] was to neutralise him but there are different players in the Brazil squad who have great quality and they have shown that on the pitch.
"Of course, it was a strategic, psychological type of discipline and I am very proud of the discipline with which my team played and they did everything we talked about, which was very important in one-on-one situations but also collectively against this opponent.
"We were not actually able to implement it in the first half and that invited Brazil to be dangerous. As far as yellow cards are concerned there were a bit too many. I didn't see any bad fouls. My team played it very cleverly. We did some good things and I'm pleased.
"I hope people will start taking notice of us. Sometimes there is a lack of recognition and that's a pity because we played very well and only conceded once. We demonstrated that this team always believes in itself and we will continue to play with that consistency.
"Tomorrow we will recover a bit and then focus on the very difficult match coming up against Serbia."
Gabriel Jesus also saw a penalty appeal fall on deaf ears after tangling with defender Manuel Akanji in the penalty area, with Petkovic backing both decisions.
"The opponent's defensive players were not well-positioned – it wasn't a foul," Petkovic said of Switzerland's leveller.
"I didn't see the penalty but I don't complain because we have referees outside and inside the field. I saw it as a very clear situation."