First-half goals from Neymar, Marcelo and Gabriel Jesus set up a comfortable win for the Selecao, who next face England at Wembley on Tuesday.
Saints' Yoshida was penalised for a rugby-style tackle on Manchester City's Fernandinho, with Neymar popping home the resulting spot-kick.
But the defender did almost redeem himself when he curled a free-kick onto the crossbar from 25 yards via a slight deflection.
Tomoaki Makino's header gave the Samurai Blue some consolation at the Stade Pierre-Mauroy.
Dusan Tadic also played the full 90 minutes as Serbia beat China in a friendly, also on Friday.