Marquez lapped the 5,403-metre Brno circuit in 2.753 mins using slick tyres, which most of his opponents did not dare to employ, earning himself the 86th pole position of his career on Saturday.
This was Marquez's 58th MotoGP pole position, which enabled him to equal the pole position record held by Mick Doohan of Australia, reports Efe news.
But it was not easy for Marquez as the track was wet in many spots and it started to heavily rain.
A bold Marquez, however, decided to use the slick tyres and subsequently he posted two consecutive fast laps.
He dominated the qualifying rounds as he had done during the fourth and final free practice session.
With an impressive rhythm he displayed during his 12 laps, Marquez set the pace in the second to last one, when he posted 2:03.779 mins, taking a 0.703s-lead over his direct rivals Spaniard Maverick Vinales (Yamaha YZR M 1) and Italy's Andrea Dovizioso (Ducati Desmosedici GP19).
It was just a taste of what was about to come.
As the first qualifying round, the KTM riders tried their best, which enabled Spaniard Pol Espargaro and Frenchman Johann Zarco to lead the timesheet.
By the end of the session, Zarco set the pace, making the cut to the second qualifying round for the first time this season ahead of his teammate Pol Espargaro.
Once the second qualifying got underway, nearly all the teams had a conservative approach due to the condition of the track.
Espargaro and Zarco were the first to post fastest laps.
Marquez's Repsol Honda, meanwhile, made a contact with Alex Rins' Suzuki as the latter surpassed the world reigning champion on their way to the pit lane.
There both employed the slick tires, which were used also by Jack Miller, Danilo Petrucci among others.
Marquez, then, rushed into the track where he posted a time of 2:04.165 mins despite the rain.
He continued to push and managed to improve his time as he covered the circuit in 2:02.753 mins to take the pole position, 2.524s ahead of Australia's Jack Miller.
Zarco will kick off the race from the first row as he came third, 2.598s slower than Marquez.
( With inputs from IANS )