Riding Gotha FRH - a horse previously ridden by his employer and multi-medallist Ludger Beerbaum - Von Eckermann finished ahead of François Mathy Jr, who won the Masters on Saturday, with D’Atlantique Royal.
"I am very happy, Henrik was just faster," Mathy Jnr said.
Another Swede, Jens Fredricson, came in third and now stands in fifth place overall with 37 points.
One more good placing and he and his Olympic horse Lunatic will secure their entry to April's finals in Gothenburg.
The next showjumping World Cup qualifier is on January 20 in Leipzig.