The two sides entered the contest at Estadio Jose Alvalade level on four points apiece after two rounds of fixtures, and it was Portugal who took control at the summit.
Joao Cancelo blasted the home side in front from a tight angle and Goncalo Guedes added a second before half-time, with both goals assisted by Bernardo Silva.
The Czech Republic was unable to find a route back into the contest as it was leapfrogged by Spain – 1-0 winner over Switzerland – in second place.
Portugal had to see out a spell of early pressure, with Michal Sadilek volleying over from a good position, before taking a 33rd-minute lead.
Cancelo, who rounded off the scoring in Portugal's 4-0 win over Switzerland last weekend, took a pass from Silva in his stride and fired past Jindrich Stanek into the far corner.
Silva played in Guedes for Portugal's second, the Valencia winger picking his spot beyond Stanek to leave the Czech Republic with a mountain to climb with 38 minutes played.
Diogo Jota was denied by Stanek as Portugal attempted to extend their lead further and Guedes had a strong penalty appeal rejected when challenged by Sadilek in the box.
Cristiano Ronaldo was also thwarted by the opposition keeper, while Adam Vlkanova missed a big chance at the other end after a mix-up, but Portugal comfortably saw out the win.