First-team regulars Pereira and Lima missed Benfica's 4-1 win over Moreirense in the Taca de Portugal on Saturday.
Uruguay international defender Pereira was rested by Benfica coach Jorge Jesus after playing against Costa Rica and Chile midweek, while Brazilian striker Lima missed the cup clash due to injury.
But the pair are set to make the important trip to Russia with Benfica's qualification hopes on the line in Group C.
"Maxi Pereira arrived a few days ago, made two appearances for Uruguay, was tired but will be an option in Russia," Jesus told reporters post-game on Saturday.
"Compared to Lima, who had a problem during the week and did not want to risk it."
"We are the champions, anything can happen," the 60-year-old added. "We know that if we lose, we are out.
"Let's play the game and try to be better than them."
Zenit also head into Wednesday's showdown at the Stadion Petrovski in winning form.
Villas-Boas was pleased with the performance and he is hoping it inspires a "set of wins".
"The Champions League is very tight, all teams depend on themselves," Villas-Boas said afterwards on Saturday.
"We know we have to play well and we know how difficult it is and we don't need anyone to remind us. Hopefully this is the start of the next set of the wins, but it is difficult.
"Now the focus is on Champions League and we will take it game by game."
