However, the Spaniard comeback king continued to break records, as his 395 points after Sunday's race are the highest scored in a single MotoGP season. Marquez's compatriot Jorge Lorenzo, who held the previous record by amassing 383 points in 2010, also returned to points with a 14th place finish in Sepang.
There was no stopping Marquez who bounced back from his biggest crash of the year to put in a champion's performance. The 55-time MotoGP race winner gained six positions in the first two corners alone and ended the first lap in second place.
With nine places gained, the reigning world champion settled in behind Jack Miller for a short while. After muscling past the Australian, Marquez began to work on closing the 1.6 second gap with Vinales.
With the gap not reducing after several laps, Marquez eased his pace to take a well-earned second place in the blazing Malaysian heat.
The result in Malaysia also earned Marquez the honour of being the first rider in history to score 17 MotoGP class podium finishes in a single season, extending his unbroken run of top two finishes to 15. Marquez's last finish outside of the top two came at the Czech GP in 2018 when he finished third.
"It was an incredible race, a great first lap. Maybe the best of my career, alongside Mugello 2015 I watched that lap last night to see what I did! It was a very nice first lap, but unfortunately the tyre dropped a lot in those first three laps and I lost a little time with Miller.
"Vinales was faster than us today and the target was the podium. I tried to do like in Phillip Island and stay right behind him but the gap was too big at 1.1 seconds and I made a mistake and dropped back.
"I'm happy with my race, but you can't imagine how happy I am for my brother's victory he deserves it so much. It's an incredible day but we also have to remember Munandar, a young and talented rider who we unfortunately lost. A big hug to his family and friends," Marquez said after the race.
The race proved to be more difficult than predicted for Jorge Lorenzo, but the Repsol Honda Team rider was able to return to the points for the first time since Misano with a 14th place finish.
Repsol Honda Team now sit just two points behind Ducati in the Team Championship with one round still to go.
Both Marquez and Lorenzo will attend Honda's EICMA presentation in Milan. Then, after an intense period of four races in five weeks, teams and riders are afforded a week off before the final round of the 2019 MotoGP World Championship begins in Valencia on November 14.
( With inputs from IANS )