Arsenal striker Aubameyang and influential midfielder Mario Lemina of French side Nice both left Cameroon to return to their clubs last Monday, with Neveu saying at the time it was to allow both players to continue their recovery from Covid-19 infections.
Neither played a minute at the tournament but Gabon still made it through their group and took Burkina Faso to extra time and then penalties despite being reduced to 10 men midway through the second half in Limbe.
"If you take out two top-level international-class players, one of whom has been the top scorer in Germany, in England and in France, then inevitably you lose assets," veteran Frenchman Neveu said.
Aubameyang and Lemina tested positive just four days before Gabon's opening game against the Comoros, then tested negative ahead of the 1-1 draw with Ghana in their second match but were again left out of the team after some residue from their infection was detected.
They were released to return to their clubs before the Panthers' final group match against Morocco.
Both were reported to be in fine health after rejoining their clubs, and French newspaper L'Equipe on Sunday reported that the duo had been allowed to leave the squad after deciding to leave their isolation for a night out in Yaounde.
"It was an extremely complicated situation. They had to stay in their rooms because they had a cardiac inflammation, but then they go back to their clubs and there is nothing," Neveu added.
"What do you want me to say? We tried to make up for losing them but you can't just replace international-class players like that."
Gabon, who lost 7-6 in the penalty shoot-out after Sunday's game ended 1-1, have still never won a knockout tie at the Cup of Nations.
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