First-half goals from Christian Pulisic, Ruben Loftus-Cheek and Rafael Leao helped Milan ease past the Czech side with a 7-3 aggregate win in the last-16 tie.
The seven-time Champions League winners will find out their opponents for the quarter-finals in Friday's draw, with unbeaten Bundesliga leaders Bayer Leverkusen, Liverpool and Benfica among the contenders. AS Roma, Atalanta, West Ham United, and Olympique de Marseille complete the strong field in the last eight.
"The level of opposition will go up now, although Rennes and Slavia Prague are decent teams even if they are not the biggest names," Pioli told reporters.
"Now the level will be higher so we have to raise the bar. There are many things we can improve on... less distractions and there are other situations to analyse in order to improve.
"Whoever we draw will be a top side but none of them are unbeatable."
