Prandelli's team trailed 1-0 to the Czechs at Juventus Stadium in Turin but two goals in three minutes from Giorgio Chiellini and Mario Balotelli - the latter from the spot - saw the home side lock up their spot in the World Cup finals in Brazil next year with two qualifying matches remaining.
It was not all smooth sailing for the Italians on Tuesday, though, as they went into the interval trailing courtesy of a fine Libor Kozak goal in the 19th minute but Prandelli said he encouraged his team to keep persisting with their attacking methods.
"The great quality of this team is that they are always able to give their best," Prandelli said.
"Tonight there have been moments in which we have suffered from a physical point of view but everyone has given the right answers.
"I believe we have made a great performance. In the first half of the match we conceded the opposing team to counterattack but we created four goal opportunities and found the right rhythm.
"We were making a good performance but we were losing 1-0.
"During the break no one had the willingness to laugh and I said to my guys that, in order to win the match, they had to keep on playing as they had played in the first half of the match."
Balotelli missed a flurry of gilt-edged chances shortly after Kozak's opener but Prandelli chose to focus on how the AC Milan man responded; eventually scoring the winner from the penalty spot.
"As far as Balotelli's episode is concerned, sometimes forward players can make mistakes," the 56-year-old Italian said.
"He was in the right position and created four or five opportunities.
"He has remained focused and concentrated and he has been rewarded for this, as in the second half of the match he has made important things for the team.
"This episode represents an additional experience for him and it's only through experiences that you can improve."
Prandelli said while he was not going to necessarily experiment with his starting XI between now and Brazil, as he wanted to build confidence in their final qualifying games and subsequent friendlies before the World Cup.
"As far as the future is concerned, now that we have qualified, I have to evaluate certain players in a particular way," Prandelli said.
"I'm relaxed as we have enough time to do this.
"I don't want to make any experiments, because I want my team to enter the pitch and be able to achieve a positive result and I also want to let certain players improve."
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