Vasco's victory gave them an identical record to Paraguayan side Libertad after four matches. They both have seven points and scoring records to share the lead in Group Five.
Juninho, a second-half substitute, broke the deadlock eight minutes after coming on when he shaped to cross from a tight angle on the left but instead squeezed the ball between the goalkeeper and near post in the 53rd minute.
Former South American champions Vasco, who had drawn 1-1 with Libertad in Asuncion last week, scored again through striker Alecsandro eight minutes later.
Inter, who won the second of their two Libertadores Cup titles in 2010, scored a late equaliser for a 1-1 draw away to Bolivia's The Strongest at 3,600 metres altitude in La Paz in Group One.
Both sides have seven points from four matches with Inter top on goal difference. Holders Santos can overtake both with a home win over bottom team Juan Aurich of Peru on Thursday.
The Strongest shocked Inter by going in front with the first attack of the second half, a low cross from the left evaded two defenders and striker Rodrigo Ramallo slid in to poke the ball home.
Inter, who crushed The Strongest 5-0 at home last week, equalised with two minutes remaining when substitute Gilberto missed the ball with his first swipe but made no mistake with his second chance and stabbed it into the net.
Club President Giovanni Luigi regarded the draw as a victory given the tough conditions at high altitude.
"The result was good because we can still finish first in the group. We couldn't leave here with a defeat, because then we'd have to win our two remaining matches," he told reporters.
Inter host holders Santos and also have to travel to face Peruvian champions Juan Aurich.
Corinthians, still looking to win South America's elite club competition for the first time, beat Cruz Azul 1-0 in Sao Paulo and leapfrogged the Mexican side into first place in Group Six. The Brazilians have eight points to Cruz Azul's seven.
Midfielder Danilo headed home Alex's free kick in the 35th minute for the only goal of the game. The Mexicans had defender Fausto Pinto sent off in the 70th for a second booking.
