Former Milan strikers Marco van Basten and Filippo Inzaghi were involved as the club celebrated its 125th anniversary ahead of kick-off, but the goalscoring instincts of those two club greats were lacking as Milan failed to convert numerous chances against Genoa.
"I think we played a good game and created a lot," Fonseca told DAZN.
"The players wanted to win, but we just lacked the goal and also the quality in the last decision. The game was played with a good attitude, we recovered many high balls. We had 22 shots, we lacked the goal.
"We were aggressive without the ball, arriving many times close to Genoa's area. It's not a question of confidence, but of the quality of the last choice."
The Portuguese coach refused to pin the blame on his attackers.
"We have good strikers," Fonseca said.
"(Tammy) Abraham suffered a blow, he didn't come out to play the second half. Alvaro (Morata) hasn't trained all week."
Morata, who replaced Abraham at half-time, fired a good chance over in the 76th minute before hitting the bar three minutes later.
"Sometimes we talk about forwards, but our game has also lacked quality in crosses and shooting. I have total confidence in our forwards," Fonseca added.
Milan, who have won one of their last five league games, were booed by the fans as they left the pitch.
"It's normal for this to happen," Fonseca said.
"We wanted to win for our fans who are always with us. Today we can all recognise that the team gave everything: I'm dissatisfied with the result, the fans too and I understand them."
Milan next travel to Hellas Verona - who are one point above the relegation zone - on Friday before ending the year at home to struggling AS Roma on December 29.