New signings Taylor Harwood-Bellis and Modou Keba Cisse were the other notable exclusions from the Villa squad for their eight league phase games, including clashes against Paris Saint-Germain and Barcelona.
Madjo announced himself in style by scoring in a superb performance as Villa narrowly lost the UEFA Super Cup final to PSG last month, but an injury has kept the teenager out since.
"It's hard for the decision we took and for the players too," Emery said ahead of Saturday's trip to Hull.
"We decided trying to analyse everything deeply. Taylor signed here for a long time. He stays here for a long time, and hopefully they will have again opportunity to play in Europe with us. Hopefully after January, maybe, or the next years.
"Madjo is 17 years old, still being so, so young, and of course he will have more opportunities to play with us this year or the next year in Europe."
Another of Villa's new signings, Johan Manzambi, is yet to make his debut due to a knee injury, but Emery is hopeful the Swiss international may be fit for next week's Champions League opener against Club Brugge.
"He is training with the group and he is professionally getting better, feeling good. But he will need some days more," he said.
The spine of the Villa side that ended a 30-year wait to win a trophy by lifting the Europa League last season has been decimated by the departures of Ollie Watkins, Youri Tielemans, Ezri Konsa, Morgan Rodgers, Emi Martinez and Lucas Digne.
Emery's men have made a slow start to the season as a result, losing their opening two Premier League games to Brighton and Arsenal.
