Gabriel Jesus played 64 minutes of the game, which was settled by Lyon midfielder Lucas Paqueta’s winner on 72 minutes after he collected a pass from Neymar and drilled home from just inside the box.
Ederson was on the bench for the game in Sao Paolo, with Liverpool’s Alisson preferred on this occasion.
The CONMEBOL qualification group sees the top four nations qualify automatically with the fifth-place team going into an inter-regional play-off.
Brazil have now won 11 successive qualifiers – a new South American record – as kept a 10th home qualification clean sheet in a row, which is also a new record.
Gabriel has now won 51 caps for his country.
Meanwhile Algeria have now qualified for the third round stage of CAF World Cup qualification and will go on to play one of the other nine countries who have also progressed in a home and away head-to-head.
A 4-0 win over Djibouti in Cairo means Riyad Mahrez's side are closing in on Qatar 2022, but will face stiffer competition in the play-offs.
Mahrez, winning his 69th cap, started the game on the bench, coming on at the start of the second-half in a match that was as good as over by the break thanks to goals from Youcef Belaili, Said. Benrahma and Sofiane Feghouli.
Islam Slimani completed the scoring three minutes from time, meaning former City player Djamel Belmadi has now lost just one of his 36 games in charge of the national team.