The Belgian from Omega Pharma Quick Step beat Giacomo Nizzolo (Radioshack-Leopard) and Roberto Ferrari (Lampre-Merida) to the line at the end of the 176.4km trek from Saint-Maurice.
It was Meersman's third World Tour victory of the season after winning two stages at the Volta a Cataluyna while Chris Froome retains the overall lead after finishing safely in the peloton.
The British rider from Team Sky won Tuesday's opening prologue in the six-day Swiss event to hold a six-second lead on GC.
There was an early attack by Julien Bérard (Ag2r-La Mondiale), Gari Bravo (Euskaltel-Euskadi) and David Veilleux (Europcar). They opened up a maximum lead of 4:45 as the riders crossed two third category climbs at Chatel-St-Denis and Martherenges.
That lead was whittled down and they were caught on the 1174m Col du Mollendruz inside the final 40km.
Matthias Brandle went away as the peloton tackled a steep descent back into Lausanne and was joined by Jeremy Roy. They lead by 28 seconds with 10km to go but the sprinters' teams worked to bring back the escapees to set up a bunch sprint finish.
Mark Cavendish was not spotted in the bunch going into the final kilometres because of a mechanical at the bottom of the last category two climb so it was left to his 27-year-old team-mate to take the victory, storming away after the BMC lead-out team failed to maintain momentum.
"It was a difficult stage," Meersman said. "The team worked perfectly. It was hard in the final, at 500 meters to go I had to brake. But then I found my good legs and saw a way to the victory.
"The goal today, if Mark Cavendish was still there after the last climb, was to go for him. If not, it would be a final for me. Unfortunately Mark had a mechanical and at that point we went for me.
"I was a little bit closed at 400 meters to go, but I managed to stay in the front. Peter Velits brought me to the wheel of Matthew Goss (Orica Green-EDGE) but when I saw the possibility to pass in the chaotic sprint I didn't wait. I decided to go by myself and not to wait for someone else to launch.
"I did my sprint and if they passed me, no problem, but if not I could win. I'm in good condition if I can win a sprint like that, against riders such as Goss and others. My goal is to possibly go for another stage tomorrow or the day after. You never know."