But Junior believes qualification is still possible as he said: "They have clinched this result here and we can get the same in
"We know it is not easy, but we have what it takes."
Striker Barcos gave Palmeiras a promising advantage ahead of the 22
Botafogo started brightly but failed to finish the opportunities it had, with Andrezinho hitting the post.
However, two minutes after the break, Barcos chested down an Artur cross and thumped past goalkeeper Jefferson to give Palmeiras the lead.
The host looked to consolidate the advantage and it duly added a second thanks to Barcos' left-footed strike.
Barcos told Folha de Sao Paulo newspaper that the team cannot afford to rest on its laurels.
"I love home and away ties. I love this type of competitions, but nothing is defined yet," he said.
Sao Paulo celebrated a 2-0 away win at tournament debutant Bahia.
The keeper told Folha: "It is an important result. We took a good lead in order to play at home in the return game. We are growing up as a team, we mark better.
"We were calm enough to play with the ball close to our feet. We must keep doing our best every day."
In Goiania, striker Washington Sebastian Abreu rescued a 1-1 draw for Figueirense at Atletico Goianiense.
Abreu equalised in the 69th minute after Marcio had put the host in front with a 37th-minute penalty.
FIFA president Sepp Blatter says accusations security officials pulled guns and beat players at the final of the Copa Sudamericana in Brazil is a warning to organisers as the country prepares to host the 2014 World Cup.