The Porto boss will be hoping the in-form Spanish side will be able to do his side a favor against Zenit, despite resting its key players after sealing top spot in Group G.
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 matches.
Fonseca's side could do with Atletico doing it a favor by 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 group winners.
"Even with all absences, I believe Atletico will go to Russia with the clear intention of winning," Fonseca said. "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 it is to stand any chance of securing Champions League progression.
"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," he said. "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 has won only one match and drawn three of its last four matches in all competitions coming into the game.