The Russian champions are looking to reach the quarter-finals for the first time, but Jonas's late winner in the first match means Benfica have the advanatge.
Villas-Boas's return to his native Portugal was Zenit's first game after the lengthy Russian winter break, and this tie takes on extra significance after a poor start to their league title defence.
With so much at stake, Villas-Boas expects his men to be ready to take the game to their opponents.
"It's a historic moment for Zenit. The quarter-finals of the Champions League is our dream, it will be a major event for Russian football," he said on Tuesday.
"And of course, this special emotion and the support of our fans will help us on Wednesday.
"Benfica are always very compact. They have good togetherness. It is always difficult to find space in how they set up defensively, but we must do that."
Italian full-back Domenico Criscito was sent off in the first leg and so is suspended for the game at the Petrovsky Stadium, as is midfielder Javi Garcia, who picked up a third booking of the tournament in Lisbon.
But former Chelsea, Tottenham and Porto boss Villas-Boas is confident in his squad's strength in depth.
"We will have to play without Criscito and Javi Garcia but it is necessary to look beyond that," he said.
"All the other players are ready for the deciding match. They are in good physical condition, they're all motivated and I hope Zenit will perform at their best in front of our home crowd."
Zenit have only scored once in three outings this year and need to hit the net to have any chance of progressing.
"We've had some match practice which we had been lacking in our previous games," Villas-Boas added.
"I believe tomorrow we will manage to stop our goal draught."
Benfica coach Rui Vitoria insisted, though, that his side would not sit on their lead, instead hoping to grab a potentially vital away goal.
"Of course we will need to pay attention to our defence. But we should never forget about the attack because it's very risky to concentrate totally on defence against Zenit," he said.
"We respect Zenit very much and on Wednesday we will come onto the pitch extremely concentrated. But we believe in our capabilities. We know exactly what we will do to achieve our goal -- to advance into the last eight."
Vitoria added that his side would not be affected by the game coming so soon after a hard-fought 1-0 derby win at title rivals Sporting on Saturday.
"We beat Porto ahead of the first match with Zenit. Now we have defeated Sporting ahead of the return leg," he said.
"It's not easy to play two matches in a row against such strong opponents but we're ready for it and I believe tomorrow we will manage to continue our winning run."
The last time these two sides met in Russia saw a 1-0 win for Zenit in the 2014-15 group stages, and a repeat result this time round would send the match to extra-time.