Joao Cancelo and Goncalo Guedes were on target in the 33rd and 38th minutes in Lisbon as Portugal continued their strong start in the competition with a comfortable 2-0 win.
Victory means they sit two points clear of Spain, having won two and drawn one of their opening three games.
The Czech Republic started the match level on points with their opponents but drop to third, after Spain defeated Switzerland 1-0 in Geneva.
The Czech Republic travel to Spain on Sunday while Portugal will have the chance to extend their advantage when they play away at Switzerland, in what has been an encouraging couple of weeks for Fernando Santos’ side.
Portugal had to go through the play-offs to qualify for the World Cup in Qatar, beating Turkey and North Macedonia to avoid an embarrassing exit.
But this convincing win came after they claimed a 1-1 draw away against Spain in their opening fixture before thrashing Switzerland 4-0 in the second, with Cristiano Ronaldo scoring twice.
Cancelo also got on the scoresheet there and the Manchester City defender made it two goals in as many matches by scoring just after the half-hour against the Czechs.
It came from some brilliant work by Bernardo Silva, who wriggled free on the right and found his City teammate inside him, who fired in.
Five minutes later, it was two and again Bernardo was at the heart of it, sliding through Guedes, who swept a superb finish beyond Jindrich Stanek.
The Czechs looked dangerous on the break in the second half and a goal might have made a game of it but Vaclav Jurecka shot wide when they had a three against two.
Ronaldo almost added a third for Portugal but his first effort of the game was saved by Stanek.