Brabec, who is in his fifth Dakar and had been leading when he retired with an engine failure last year, has taken the overall lead with a win in Stage 3 and never surrendered it, placing in the top five in all but one of the remaining stages.
The one exception was the penultimate day when Pablo Quintanilla was able to close the gap from 25 to 13 minutes ahead of the shortened last stage.
Though he retained a comfortable lead still, Brabec did not ease up on the final day as he fought for the stage victory against teammate Jose Ignacio Cornejo.
He ultimately lost out to his fellow Honda rider and settled for second on the day by 53 seconds, which was enough to clinch the title by 16m26s.
Husqvarna rider Quintanilla secured his best Dakar result yet in second as he took a fourth top-four result in six years.
Toby Price was KTM's top representative in third, the Australian maintaining his superb record of being a top-three rider every year he finished the event.
Price missed out on the top spot by 24m06s, followed by Cornejo and teammate Matthias Walkner.
Joan Barreda (Honda) took seventh, a 15-minute penalty for a penultimate-day engine change ultimately costing him one position to KTM's Luciano Benavides.
Franco Caimi was the top Yamaha in eighth, followed by Husqvarna duo Skyler Howes and Andrew Short, the pair making it three American riders in the top 10.
Final Standings (Bikes, Top 10):
Jose Ignacio Cornejo