The 47-year-old is still recovering from a stroke five months ago and felt compelled to tell Vasco fans he will not sign a new contract until he feels 100 percent fit to return to work.
Nacional surprised Vasco 2-1 at their San Janaurio ground in Rio de Janeiro in the opening Group Five match with assistant coach Cristovao supervising.
"The Vasco management insisted I signed a contract renewal at the end of last year but I'm only going to sign when I'm 100 percent," Gomes, who required brain surgery, told the club's website.
"It was my choice. We have a verbal agreement and I consider myself Vasco's trainer," added Gomes, who had a stroke while on the bench during the Rio derby against Flamengo in the Brazilian championship on August 28.
Midfielder Juninho, who helped Vasco win the Libertadores Cup in 1998 before spending eight successful years at Olympique Lyon, praised three-times champions Nacional for their performance.
"Their team were very good, they marked our buildup and were quick to attack. Our team play a possession game and find it difficult to counter-attack," he told reporters.
Nacional's Marcelo Gallardo, in his first season as a coach having hung up his boots in June, was thrilled with his team's "historic triumph".
"They tell me Nacional had not won in Brazil for four decades in the Libertadores. This is magnificent," the former Argentina international told the Montevideo daily El Pais.
"Against Brazilians we generally suffer, so we had to be dynamic and defend as far from our goal as possible."
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