The Petronas Sprinta Racing Team rider, who crashed at Turn 3 in the first session, came back strongly after using the slipstream generated by teammate John McPhee to post 1:45.879 for his best opening-day performance of the season.
Khairul will be hoping to ride on the momentum as he seeks to win his first championship points.
“It has been a very positive day. I want to say thanks to John for helping me with the slipstream to start the lap.
“I was able to follow him and get a really good time.
“The conditions are difficult out there, it started off wet and then became a mix of wet and dry.
“We went for dry tyres in the second practice, waited for the best time on track and it worked.
“I’m very happy with today and let’s see if we can make another step forward,” said Khairul.
McPhee was fastest in the opening session and came in third (1:45.345) as the track dried up in the second session.
Meanwhile, in MotoGP, Petronas Yamaha Sepang Racing Team riders played it safe during Friday’s practice.
Franco Morbidelli and Fabio Quartararo ended the opening day seventh (1:35.369) and 11th (1:35.489) respectively.
“It was a tricky day because it was wet and cold in the morning but half and half in afternoon.
“The aim was to get used to the conditions, adapt to them and not to over-push in any area. We were fast enough to get into the top 10, which was the aim of today,” said Morbidelli.
“It will be important to see how fast we are in the dry because we know how quick we are in the wet and in mixed conditions here.”