Defender Theodor Gebre Selassie became the first Czech to score in four matches in a 3-1 victory over Malta in the 2014 World Cup qualifier on Friday.
Gebre Selassie headed in his first international goal in the 34th minute.
Roderick Briffa stunned the Czechs by erasing the deficit four minutes later with a clinical finish from the edge of the area before striker Tomas Pekhart put the hosts ahead again seven minutes into the second half with another header for his first international goal.
Jan Rezek put the result beyond doubt with a low shot in the 67th.
Goalkeeper Petr Cech saved a penalty in the final minute.
The Czech Republic has four points from two matches in Group B while Malta is without a point.
The Czechs next play Bulgaria on Tuesday.
