Atletico Madrid defeated Porto 2-0 on Wednesday, which ensured Fonseca's team would miss out on the Round of 16 behind the Spanish club and Zenit St Petersburg.
Porto had 10 shots to Atletico's five at the Estadio Vicente Calderon in Madrid but hit the frame of the goal four times, while they also had a penalty saved.
But Fonseca did not single out his attackers for the loss, claiming his defenders should have done better.
"We made it difficult for Atletico, we've hit the post four times and missed a penalty, but we weren't good enough in defence and Atletico were," the 40-year-old coach said.
Porto finished the group stage of the Champions League with just five points from six matches, one behind second-placed Zenit, who surprisingly lost 4-1 against Austria Vienna on Wednesday, while Atletico topped Group G's standings with 16 points.
But while Fonseca believed Porto had enough chances in Madrid to advance, the Portuguese argued it was his side's terrible home form that cost them a spot in the knockout stages.
Porto picked up just one point from their three home games in Group G.
"We're not the least bit satisfied with what we've done in the Champions League," Fonseca said.
"Not only because of this defeat, but also with our games at home."
