The Blues were second best for most of the match, although Cech did his best to keep them in the game with a number of saves in the first half.
However, Mohamed Salah grabbed the decisive goal in the 87th minute.
"We are qualified and that is the only positive as we did not play well," Cech told Sky Sports News.
"If you give your opponent in the Champions League the feeling they can win, they can win.
"First half we did not play well, and in the second half we improved. The last touch was always missing."
Chelsea qualified after Schalke drew away to Steaua Bucuresti in Group E's other game.