The result meant that the tie finished 3-3 on aggregate, but with Vasco having won 2-0 at home in the first leg, they progress to the next round on away goals.
Luan put Palmeiras in front on 13 minutes, and the hosts levelled the aggregate score when Kleber added a second on 54′.
But Vasco got their crucial away goal four minutes later through Jumar, and although Marcos Assuncao made it 3-1 to Palmeiras in injury time, it was too little, too late.
Vasco will now play either Club Aurora of Bolivia or Paraguay’s Nacional in the next round.
