The Portuguese outfit drew 1-1 at home to Austria Vienna on Tuesday to leave them in third place in Group G, a point behind Zenit St Petersburg.
Roman Kienast had given Vienna the lead in the 11th minute for their first ever Champions League goal before Jackson Martinez earned his side a point three minutes into the second half.
Porto could not find a winner, and the draw means they must now win at already-qualified Atletico Madrid on matchday six, and hope that Zenit fail to win in Austria.
After the game, Fonseca conceded it would be difficult for his men.
"It's hard for us to enter the last game in this situation," he said.
"We had the possibility of entering that game depending only on ourselves, but now we have to win in Madrid and wait to see what happens in the other game."
Of the game itself, Fonseca rued the poor start made by his side.
"We suffered a goal with 10 minutes played, which unsettled our team," he said.
"We offered the first 45 minutes to our opponents. In the second half we pressured and we created several chances to score.
"But the fact is that we were not able to accomplish our goal, which was to win this game.
"Despite not being at our best in the first half, we reacted well against a team that played with their lines deep in their own half."
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