Patrik Indra and Lukas Vasina scored 22 and 21 points for the Czech Republic respectively, while Poriya Hossein Khanzadeh and Ali Hajipour earned 18 points each for Iran.
The Czech Republic will play the US and Bulgaria winner in the semifinal round.
In the other semifinal match, Poland will face Italy.
Italy is the defending champion, having won its fourth title in 2022.
Taking place in Manila, the Philippines, the championship features 32 teams from across the world competing for the coveted title.