The 28-year-old Cannondale-Drapac rider had tried to ride away from his breakaway companions Naesen, Jasper Stuyven (Trek-Segafredo) was third ahead of Jens Keukeleire (Orica-Scott) and Nathan Van Hooydonck (BMC) without success in the closing kilometres.
In the sprint for the line, Van Hooydonck was the first to move before Vanmarcke went long, only for Naesen to use his slipstream and take the win in a photo finish.
"Sep started from far out and had a good gap. He did what I did in E3 Harelbeke, while I did what Greg did. I was in the slipstream and came over him on the line. Hopefully this is my breakthrough victory. I knew I was ready for it," Naesen said of his win.
Vanmarcke described the day's racing, explaining that he believed his best shot for victory would come from a late attack.
"My race was a city course, like a kermesse, with a lot of corners and a few cobbled sections. The entire race, all 5.5 hours, was stressful because you always had to be in position," he said in a team release. "The final opened after 190 kilometers, with 50 kilometers left. We got away with 17 riders. By the last lap, we where left with only five.
"I attacked in the last kilometers, but I wasn’t able to get away. At that point, Ken [Vanmarcke], my sport director, advised me that I needed to surprise them and sprint from far. It was my best option, so that’s what I did."
While he wasn't confident in a sprint finish, Vanmarcke added that he thought the title was his only to be disappointed at the last possible moment,
"I thought I was going to win as we sprinted to the line, but in the very last meters, Naesen came up and won. He finished 1.2 centimetres in front of me," said Vanmarcke.
After crashing out of the Tour of Flanders, Vanmarcke has been building back up to form which was on show at the Hammer Series. He explained that after his injuries and illness at the start of the season, to have come so close to a breakthrough national title brought up mixed emotions.
"While I'm happy with the level I have again after all the problems in the spring, I’m also really disappointed because I was so close to becoming national champion and wearing the colors of my country for a year," he said.
Vanmarcke will next be in action at the Tour of Austria with the stage race starting July 2 and running through to July 8.