First-half goals from Hulk and Axel Witsel saw Zenit assume early command of UEFA Champions League Group C.
Brazil international Hulk broke the deadlock after just five minutes, silencing the Estadio da Luiz crowd with a sumptuous dink over goalkeeper Artur.
Artur was later sent off in the 18th minute for hauling down Zenit captain Danny, virtually ending Benfica's hopes of salvaging anything from the match.
And Zenit made the most of their numerical advantage through Witsel's header four minutes later as Benfica crashed to their first home defeat in 52 matches.
"The first half was good for us. Benfica struggled after the red card. In the second half we wanted to get the third, but we always controlled the match," said Villas-Boas.
"We had some chances that we missed but Benfica could have also made it 2-1, but it's excellent to win away.
"Doing it in a hard group such as this one was fundamental, moreover in a stadium that hadn't seen a home defeat for so long.
"It was a total success to us, in a good performance, controlling the game."
The win in Lisbon gave Zenit an 11th consecutive win in all competitions, with their last defeat coming at the hands of AEL 1-0 in the third round of qualifying.
Zenit reached the round of 16 in 2013-14 but Villas-Boas insisted it was too early to be looking beyond the group stages.
"It's premature to speak about it [last 16], it depends on the result of the next match," the Portuguese tactician said.
"If we beat Monaco then we could be in a good position to go through. In an even group it was important to score points away. Let's see what we now do at home."
