Gabriel got the winning kick for Brazil after Gustavo Gomez and Derlis Gonzalez missed for the visitors. Roberto Firmino pulled his spot kick wide for the hosts.
Brazil coach Dunga blamed a virus that hit several players for his team's early elimination from the Copa America at the hands of Paraguay on Saturday.
Argentina captain Lionel Messi pulled his side level in the 57th minute after a handball by Paraguay's Ivan Peris which no-one on the pitch appealed for but was spotted by a VAR review.
Derlis Gonzalez slotted two penalties, one in regular time and again in the shootout, to help Paraguay beat Brazil 4-3 after a 1-1 draw on Saturday that advanced them to a Copa America semi-final against Argentina.
Uruguay made light of the absence of striker Luis Suarez to recover from a goal down and beat 2015 Copa America hosts Chile 2-1 in a friendly in Santiago.
Celebration was tinged with disappointment for Manchester City who eased into the Champions League quarter-finals for the first time on Tuesday but lost Vincent Kompany to injury in a 0-0 draw with Dynamo Kiev.
Holders Real Madrid chased away some of their early-season blues when Gareth Bale scored the pick of the goals in a 5-1 rout of FC Basel in their Champions League Group B opener on Tuesday.
Argentina and Brazil both lost their opening World Cup qualifiers on Thursday as the South American campaign for Russia 2018 started in unexpected fashion.
Christian Pulisic scored his 10th goal for the United States before being substituted after picking up a knock in a 1-1 draw with Chile in a friendly in Houston on Tuesday.
Holders Real Madrid chased away some of their early-season blues when Gareth Bale scored the pick of the goals in a 5-1 rout of FC Basel in their Champions League Group B opener on Tuesday.
Cristiano Ronaldo ended a three-game goal drought as Real Madrid won 2-0 at Schalke.
Thomas Meunier volleyed a spectacular last-minute goal to give Paris St Germain a 2-1 win at FC Basel, which took them into the last 16 of the Champions League on Tuesday.
Barcelona's Luis Suarez hit a brace and set up a double for a spritely Lionel Messi to score in his first start after injury in a rampant 6-1 Champions League victory over AS Roma on Tuesday.
Neymar shrugged off some rough tackling and a missed penalty to score a brilliant solo goal as he led Brazil to a 3-0 win over Paraguay that moved them within sight of the 2018 World Cup finals on Tuesday.
Jose Mourinho suffered a nightmare homecoming as Porto, the club he led to the Champions League title in 2004, inflicted a 2-1 defeat on his woefully out-of-sorts Chelsea side in Group G on Tuesday.
Karim Benzema came off the bench to score 13 minutes from time and ruin any chance of a dream result for resilient Ludogorets as holders Real Madrid carved out a patchy 2-1 win in Wednesday's Champions League Group B match.