The 21-year-old Frenchman took advantage of a ricochet in the box to drill a low shot into the bottom left corner on 40 minutes.
Town skipper Peter Clarke had tried to clear the ball and it hit Helan amid claims of handball but the midfielder stroked the ball home.
Helan was infamously booked twice when the sides played out a 0-0 draw in December 2012 but was not sent off.
The referee that day, Mick Russell, wrongly put the name of Helan's team-mate Michail Antonio down for the first booking.
Helan, who was on loan from Manchester City at the time, signed permanently for Wednesday last summer.
Sam Hutchinson then set up Jacques Maghoma on 72 minutes for a close range finish and complete a smash-and-grab raid on their Yorkshire rivals.
Full-back Hutchinson, 24, was making his first start since joining from Chelsea on loan on Valentine's Day.
Helan's pace caused problems on the break throughout the game, notably twice early in the second half when he hit the side netting and had a shot blocked after sprinting clear.
Huddersfield were seeking a third win in four matches but lacked punch up front despite dominating possession.
Both sides traded long-range efforts early on, with Adam Hammill forcing Owls keeper Chris Kirkland to save his 20-yard drive at the second attempt.
At the other end Gary Gardner drilled a volley just wide on 15 minutes after a clearance fell to him on the edge of the box.
However Helan's goal gave Wednesday a slender lead at half time.
Town boss Mark Robins brought on striker Joe Lolley for Adam Hammill at half-time.
Nahki Wells, who has struggled since his big-money move from Bradford, was taken off on 71 minutes.
His afternoon was summed up six minutes earlier when he squared the ball when clean through on goal - but only succeeded in passing to an Owls defender.
Lolley went close on 87 minutes when he fired just wide after Danny Ward headed down Adam Clayton's high ball into the box.
Clayton, who had scored twice in his last three outings, hit the bar in the last minute with a 25-yard effort.
And Ward headed over a a Paul Dixon cross from the left in stoppage time among a flurry of late chances.
But the visitors held on and are now unbeaten in their last nine away matches as the revival under new boss Stuart Gray continues.