Meersman won a nine-man sprint at the end of the 174km race, with Australians Simon Clarke (Orica-GreenEDGE) taking second and Nathan Haas (Cannondale-Garmin) third.
Evans (BMC), the 2011 Tour de France champion, was emotional after finishing fifth in his retirement race and said he had little chance against faster men such as Meersman and Haas.
"They're pretty quick in the finish," he said. "I was hoping to make the front group at first, but it wasn't exactly the easiest group to pick.
"In the finish, I came from a reasonably good position ... but I didn't have the legs. Even if I had the legs, those guys are just quicker than me in that kind of finish.
It was a pulsating contest, held in wet and windy conditions and reminiscent of the early season northern hemisphere races.
A group of five riders, featuring Australian domestic riders Darcy Woolley (African Wildlife Safaris), Josh Taylor (Charter Mason Giant) and Brodie Talbot (Budget Forklifts), formed early in the race and built a lead of four and a half minutes.
But disaster struck for the group as Laurent Didier (Trek Factory Racing) crashed after about 50km as he was riding alongside his team car.
He was taken to hospital with a suspected broken hand, reducing the breakaway to four riders with the resulting loss of manpower contributing to their advantage quickly eroding.
With 82km to go, Cannondale-Garmin used the crosswind to launch a withering attack that split the peloton into several groups.
Evans was among the big names who were caught out by the move, which ignited the race.
The chasers recovered and later reconnected with the break but from that point a series of constant attacks blew the peloton apart.
The race came down to three final laps of a hilly 20km circuit in Geelong.
Evans and then key rival Richie Porte (Sky) attacked near the end of the second lap, but they were marked closely.
At the start of the last lap, Evans' BMC teammate Danilo Wyss and Porte's Sky colleague Ian Stannard were at the front along with Etixx-Quick Step rider Peter Serry.
They were soon joined by Clarke and then Martin Elmiger (BMC).
The lead changed again on the last steep climb at Challambra Crescent, with the race coming down to a 10-man lead group.
After Moreno Moser's (Cannonade-Garmin) solo attack in the last six kilometres failed, he faded from the effort and the remaining nine contested the finish with the peloton approaching fast.
Cadel Evans Great Ocean Road Race: 174km, Geelong
1 Gianni Meersman (BEL) Extixx-QuickStep 4hr 15min 22sec
2 Simon Clarke (AUS) Orica-GreenEDGE
3 Nathan Haas (AUS) Cannondale-Garmin
4 Luke Rowe (GBR) Sky
5 Cadel Evans (AUS) BMC
6 Giampaolo Caruso (ITA) Katusha
7 Moreno Moser (ITA) Cannondale-Garmin
8 Danilo Wyss (SUI) BMC
9 Pete Kennaugh (GBR) Sky 0:00:07
10 Heinrich Haussler (AUS) IAM Cycling 0:00:09