The Blues, up 1-0 after the first leg in the quarter-final tie, jumped out to a quick 3-0 advantage over their visitors at Stamford Bridge through Pedro, a Simon Deli own goal and a strike from Olivier Giroud.
While Prague did cut it to 3-1, a second goal from Pedro seemed to salt away the tie just under a half-hour into the contest.
But a poor start to the second-half saw Chelsea concede twice to Petr Sevcik in the 51st and 53rd minute, making it 5-3 on aggregate and leading to a nervy final 40 minutes for Chelsea.
While the Blues ultimately saw out the victory, Azpilicueta was unimpressed with the second half, noting this is something that has plagued the squad this season.
"It is a mistake we are making very often and we are conceding early goals in the second half of games,” Azpilicueta told BT Sport. “We were 4-1 up but they put us in trouble and we were risking it. We were suffering until the end.
"It is not the way we want to win the trophy but we are in the semi-final and hopefully we can get through."
Manager Maurizio Sarri echoed those sentiments, admitting the squad struggled to begin the second half.
However, Sarri chose to focus more on his team’s success on the evening – dispatching hardworking and difficult opposition to make it to the semi-finals of the competition.
"We started very badly in the second half but I'm really really happy because we played well in the first 45 minutes and we are in a European semi-final which is very important to us," Sarri told BT Sport.
"We knew very well the match was going to be difficult. They ran a lot and with quality -