The BMW driver held off Rast through the slow first sector, taking in the Haarbocht right-hander through to the De Strubben hairpin exit, before the battle came to a close when R-Motorsport driver Daniel Juncadella stopped his Aston Martin Vantage at the side of the track.
Following the safety car called to retrieve the Aston, Wittmann made a superb restart to pull a gap of over a second to Rast’s Audi, and his victory hopes were given a boost when Rast ran slightly wide over the exit of the Geert Timmer Bocht chicane.
Wittmann would again come under threat, but not until the pitstop window, and it would be Muller who would prove to be a thorn in the side of the BMW driver.
Muller, the second-highest Audi driver in the standings, could only qualify sixth but climbed the order in the opening stint after overcoming Timo Glock in a tight battle that led to the BMW driver skating over the gravel at the De Strubben Hairpin.
Muller then made further progress by dispatching Pietro Fittipaldi and Loic Duval and extended his first stint right up until the 26th lap, pitting to emerge ahead of Wittmann and Rast, boosted by the pair reigniting their scrap after both drivers made their mandatory stop.
But in the torrential conditions, the outlap was made all the more challenging, and now second-placed Wittmann was able to make up a deficit of several seconds to get by before the run to the Meeuwenmeer kink and return to the lead.
Muller was able to get his tyres up to temperature before Rast could pass him and held onto second at the flag, making it two Audis on the podium.
BMW’s Philipp Eng was fourth after defeating Glock late on, with the ex-Formula 1 driver battling his way back through the field after his early mistake and pulled off a stunning move around the outside of Eng earlier in the race.
WRT Audi’s Jonathan Aberdein was compromised by the red flag caused by Jake Dennis in qualifying, but climbed from 10th on the grid to take sixth in the race as teammate Pietro Fittipaldi struggled in the conditions and slipped from fourth to 11th.
Jamie Green was another to rise through the field and took seventh ahead of Duval, who had impressed by qualifying third.
Mike Rockenfeller was ninth for Audi, while Sheldon van der Linde recovered to 10th after being punted into a spin at the De Strubben hairpin by BMW stablemate Bruno Spengler.
Spengler served a drive-through penalty that meant he could only finish 15th.
Local driver Robin Frijns endured a nightmare race that began with a start at the back of the field due to necessary repairs to rectify an oil pressure problem.
He climbed into the top 10 but spun off into the barriers backwards after running over a kerb, damaging the rear of the car and retiring.
Dennis was the leading R-Motorsport driver and finished 12th for the Aston Martin team ahead of Ferdinand Habsburg and Paul di Resta, who narrowly missed colliding with a hare during the race.