The 217-kilometre race was not without jeopardy with sections over rough dirt road which caught out several riders, including last year's winner and runner-up, Soren Kragh Andersen and Niki Terpstra, who were both taken out while leading.
High winds also blew the race to pieces and Wallays attacked from a long way out, helped by the punctures for those ahead but nevertheless forced to work hard in a solo effort that was rewarded by his first one-day win since the 2016 Grand Prix Pino Cerami.
Terpstra did fight back from his puncture to finish on the podium in this race for the fourth time in eight years while Oliver Naesen was behind him in third, sitting up in the final metres out of recognition of the work the Dutchman had done to help them break clear.
Wallays - 'I was trying to make a gap, didn't plan for it to be the winning move'
"I had a good feeling from the beginning and this week," Wallays said.
"I gave it all and I had a happy ending.
"It's a totally different race now with the off-roads. The first time I won was in the early breakaway with Tommy Voeckler and we had tail winds!
"This time it was head winds and then it turned as well. Totally different."
Wallays has endured an injury-battered year, having been ill during the Vuelta and then lost three teeth in a brutal crash.
The Belgian said he had targeted the Tour de France after his misfortune but was not selected by Lotto Soudal and after his win on the mixed road conditions of the new-look Paris-Tours, could look to target the cobbles of Paris-Roubaix next season.