The Finn, driving a ŠKODA Fabia, closes the gap to series leader Andreas Mikkelsen to six points after the Norwegian crashed out on SS7, the opening stage of the day.
Peugeot driver Loix was third behind Patrik Flodin on the closing 13.39-kilometre Kemmelberg test.
Pieter Tsjoen finished third overall despite a scare on the penultimate SS17, which was won by Loix.
“I made a small mistake in the beginning when I braked too late for a junction,” he said. “I saved myself with the handbrake but only lost a couple of seconds.”
Michal Solowow was fourth in the rally ahead of Flodin and Mathias Viaene.
Hanninen was edging towards his 10th IRC win - a record – after sealing SS16 by just 0.3s from Loix.
The Belgian snatched the previous stage by 1.4s from Hanninen after going on all-out attack, but found himself still almost 40 seconds behind at that point.
That was because Hanninen took the 14th stage by a huge 11.6s from Tsjoen with Loix trailing in third.
“We were staying on the safe side with no extra attack,” Hanninen nevertheless reported after that stage.
Loix revealed the reason for the disparity in times.
“We are working hard but I knew this would be a bad stage for us because we don’t have the speed in the straight lines compared to the ŠKODAs,” he said.
Hanninen was fastest on Kemmelberg 1, SS13, despite reporting that his car’s engine kept cutting out.
“The engine was cutting a little bit but now we go to service so it will be okay,” said Hanninen, who was a mere 0.1s quicker than the time of rival Freddy Loix in a Peugeot 207.
Seven-time Ypres winner Loix won SS12, the Show Wasquehal street stage, from Hanninen with IRC Production Cup leader Andreas Aigner a sensational third fastest in his lower-specification Subaru Impreza R4 STI, 3.6s down on Loix.
Former IRC champion Hanninen won the Lille-Eurométropole SS11 – which crossed the Belgian border into France - despite admitting afterwards that he was driving “carefully” as he was not happy with his pacenotes while he also claimed the Hollebeke SS10 when Loix lost four seconds to him during an off-road moment which led to a build-up of grass on the front of his car.
Loix took stage nine from Hanninen - after the Finn displayed indecision at several junctions - and was also quickest on SS8.
Hanninen led SS7 while defending IRC champion Andreas Mikkelsen retired on that opening stage of the day after breaking a suspension arm on his ŠKODA UK Motorsport Fabia overshooting a junction and going off the road.
It was Mikkelsen’s first retirement in the series since the Canon Mecsek Rallye in Hungary last September.
“I am very disappointed to not finish the Ypres Rally, as is the whole ŠKODA UK Motorsport team,” he said.
“We once again showed good pace on a Tarmac rally, we’re still leading the IRC and we have two very strong gravel rallies in San Marino and Romania up next, so we’re still in a very strong position approaching the midway point of the season.”