The double world champion's arrival in Jeddah was delayed by a day as he battled a stomach bug.
But he showed no ill-effects as he raced to the top of the time sheets in the first running of the weekend.
Verstappen finished half-a-second clear of Sergio Perez in the other Red Bull, with Fernando Alonso third for Aston Martin. Lewis Hamilton finished sixth for Mercedes.
Verstappen crushed his rivals in Formula One's opening round of the season in Bahrain a fortnight ago to kick off his championship defence with an emphatic win.
And the Dutchman's pace in the opening action of the weekend suggests he will remain the driver to beat.
Alonso took a podium on his Aston Martin debut in Bahrain and the 41-year-old was best of the rest here, albeit seven tenths behind Verstappen.
Alonso's team-mate Lance Stroll finished fourth as Aston Martin's impressive start to the new season continued.
Mercedes arrived in Saudi Arabia in crisis mode following a turbulent opening race.
Hamilton finished fifth in Bahrain - more than 50 seconds behind Verstappen - and then accused Mercedes of ignoring him on the development of this season's machine.
Speaking on Thursday, he said his Mercedes team needs "a kick" after conceding his chances of winning a record eighth world title are over for another year.
Hamilton ended the day's opening running 1.2 sec off the pace and a place behind team-mate George Russell, who finished fifth.
Carlos Sainz was seventh for Ferrari, with team-mate Charles Leclerc, who will serve a grid penalty on Sunday for changing engine parts, 11th. Lando Norris finished 20th and last for McLaren.