Alpecin-Fenix teammate Mathieu van der Poel had led the men's peloton heading into the last kilometre, before Uno-X's Rasmus Tiller pushed in front with the finish line only a few hundred metres away.
With van der Poel's handlebar visibly broken, it was Merlier who would eventually catch Tiller - the Belgian latching onto the wheels of those in front and taking the lead at an incredible pace.
The 28-year-old completed the 205.4km event in four hours, 34 minutes and 29 seconds, followed by Tiller and Andrea Pasqualon (Intermarche – Wanty – Gobert Materiaux).
Liv Racing's Kopecky also tasted success in Belgium overnight, sprinting to victory from a reduced group at Le Samyn des Dames.
The 25-year-old beat both Emma Cecilie Norsgaard (Movistar) and Australian Chloe Hosking (Trek-Segafredo) to the line, with Kopecky saving just enough to hit the wind with 150 metres remaining.
"This is my first win in the tricolor and my first for Liv Racing," Kopecky said of her 2h 20' 04" effort.
"What a great start to the season. This is also confirmation of my good form.
"After Omloop, I was disappointed with my fourth place because I missed the podium due to a stupid mistake in the sprint. Now I've shown that the fast legs are there. I feel really good. It's nice to start like this."