Merlier's second stage win of this year's Tour mirrored the Soudal Quick-Step sprinter's photo finish victory over the Italian on stage three.
The Belgian stayed glued to Milan's wheel before unleashing his kick metres from the finish in Chateauroux after the 174.1-kilometre ride from Chinon.
"One moment I thought I was boxed in but I can come out just before 200 metres or maybe just after, I don't know anymore," Merlier said.
"I just go all in and I'm happy I can win my second stage here."
Van der Poel's day began with promise as he and Jonas Rickaert broke away early, building up a commanding lead of more than five minutes with a tailwind pushing them to speeds of more than 50 kph.
The Alpecin-Deceuninck duo persisted after taking points in the intermediate sprint for the green jersey before the peloton began their chase.
"Well, five minutes-and-a-half is a lot so we tried to help and also other teams started to help. The pacing was quite high," Merlier added.
"So they were at the front, but it was just hard for the guys in the front and the guys who were pulling and the bunch was just nervous."
However, the peloton soon began to reel in the Alpecin-Deceuninck duo to reduce the lead to less than a minute with 11 km to go, while sprint specialist Wout Van Aert was dropped.
As the rest of the Alpecin-Deceuninck team attempted to move to the front of the bunch and disrupt the chase, a tiring Rickaert finally gave in and slowed down, leaving Van der Poel to ride solo to the finish with more than five kilometres left.
The Dutchman was visibly grimacing as the chasing pack came into view behind him and his heroic effort ended in the final kilometre when he was swallowed up by the bunch.
Slovenia's Tadej Pogacar (UAE Team Emirates) retained the yellow jersey and maintains a 54-second lead over Belgian Remco Evenepoel (Soudal–Quick-Step) in the general classification.
UAE Team Emirates and Pogacar suffered a major blow, however, when mountain domestique Joao Almeida was forced to abandon the race after fracturing a rib in a crash on stage seven - just before the Tour heads into the mountains.
The 26-year-old, who finished fourth in the general classification last year, had come into the race in brilliant form having won the Tour de Suisse, the Tour of the Basque Country and the Tour de Romandie earlier this year.