The victory for former South Africa coach Joel Santa's team guaranteed Botafogo a place in the title decider for the fifth year in a row.
A header by defender Fabio Ferreira from a corner and a penalty converted by Uruguay striker Sebastian "Loco" Abreu in the final 20 minutes gave Botafogo the symbolic title of winners of the first phase of the Rio de Janeiro state championship.
Vasco had Nilton and Titi sent off for fouls on Botafogo's 18-year-old substitute Caio when they were already a goal down.
"Today's secret was the self-esteem of the squad and belief in the professional (coach) who arrived," Santana told reporters.
"(With) everyone's help, officials', fans', Botafogo became that Botafogo we all know. We managed to beat a great adversary playing a great second half."
Last month's 6-0 defeat by Vasco led to the sacking of coach Estevam Soares and the return of Santana, who had been dismissed by 2010 World Cup hosts South Africa eight months before the June kickoff of the finals.
The Carioca is one of the state tournaments that open the season in Brazil before the Brazilian championship kicks off in May.
In the Paulista (Sao Paulo) championship, Robinho's Santos lead by four points after their 2-1 win over Mirassol, their seventh successive victory.
Third-placed Corinthians are the only other team of the state's big four who are sitting in the top four places that guarantee qualification for the semi-finals.
The other two met in the weekend's big derby with seventh-placed Palmeiras beating Sao Paulo (fifth) 2-0 with two second-half goals from striker Robert on Antonio Carlos Zago's debut as their coach.
Zago left Sao Caetano on Thursday to take over from the sacked Muricy Ramalho. On Wednesday, Zago had steered Sao Caetano to a 4-1 rout of Palmeiras, which prompted Ramalho's sacking.
