Loix, racing in a SKODA Motorsport Fabia Super 2000, got to the front of the field at the qualifying stage on Thursday and never gave up the lead.
The final stage was neutralised for safety reasons after Miko Pajunen and Davy Vanneste's cars caught fire, blocking the stage and forcing the cancellation. Both crews were unharmed.
Bryan Bouffier's victory in the penultimate stage meant that he sealed second place, while Craig Breen claimed third, with both drivers using Peugeot 207s.
Breen was in fact a beneficiary of the organisers' decision - he had lost time in a ditch during his run on the stage, only to have the delay rendered immaterial by the stage's results being neutralised.
“Right from the start I had a great feeling with my car and I was able to push,” said Loix, who made his Ypres debut in 1993.
“We showed a very good speed in difficult conditions. At the moment when Craig [Breen] had problems it was a little bit slowing down and just trying to get to the finish. I am very happy.”
Final top 10
1 Freddy Loix (BEL)/Frédéric Miclotte (BEL) ŠKODA Fabia 2000 2h32m19.4s
2 Bryan Bouffier (FRA)/Lara Vanneste (BEL) Peugeot 207 S2000 +1m21.0s
3 Craig Breen (IRL)/Paul Nagle (IRL) Peugeot 207 S2000 +1m52.5s
4 Andy Lefevere (BEL)/Andy Vangheluwe (BEL) Mitsubishi Lancer Evo X +6m36.4s
5 Hermen Kobus (NLD)/Erik de Wild (NLD) Ford Fiesta S2000 +6m41.2s
6 Michał Sołowow (POL)/Sebastian Rozwadowski (POL) Ford Fiesta RRC +7m00.0s
7 Melissa Debackere (BEL)/Cindy Cokelaere (BEL) Peugeot 207 S2000 +9m38.5s
8 András Hadik (HUN)/Krisztián Kertész (HUN) Subaru Impreza R4 STI +10m09.3s
9 Antonín Tlusťák (CZE)/Jan Škaloud (CZE) ŠKODA Fabia S2000 +10m25.6s
10 David Croes (BEL)/Eric Tack (BEL) Mitsubishi Lancer Evo X +12m07.7s