The Porto boss will be hoping the in-form Spanish side will be able to do them a favour against Zenit, despite the club resting their key players with top spot in Group G sealed
The Portuguese champions, who face Austria Vienna at home on Tuesday, sit third in Group G, one point behind second-placed Zenit with everything to play for in the final two group-stage matches.
Fonseca's side would be aided by Atletico picking up a result against Zenit in Russia, but the chances of that were reduced when star players like Diego Costa, Arda Turan and David Villa were left at home to rest by the Spanish club, who have already secured their position as group winners.
Fonseca said: "Even with all absences, I believe Atletico will go to Russia with the clear intention of winning.
"We just need to focus on winning this game and then see what happened to our opponents.
"We could be in a better place than we are, but we remain in a strong position in all competitions in which we compete."
Fonseca insists his side must beat Austria Vienna if they are to stand any chance of securing Champions League progression.
He added: "At the moment, things are quite clear - if we want to think about qualifying for the next stage, or think about going to Madrid to compete for a place in the next phase, we have to win the game.
"We had trouble winning in Austria on matchday one. This is a team on the rise, with three league wins in three games and they defend well."
Porto have won one and drawn three of their last four matches in all competitions coming into the game.