The man Billy Davies signed in the summer from Luton Town just can't stop scoring and notched up his fourth in as many games as Derby turned the tables on the Owls.
Derby were heading for defeat after Chris Brunt had put Wednesday in front and substitute Giles Barnes was sent off for two bookable offences.
But former Sheffield United striker Paul Peschisolido grabbed an equaliser two minutes after arriving as a substitute and being booed on by the home fans.
And then Howard struck in added time to rob Wednesday manager Paul Sturrock of his first home win on his second anniversary in charge at Hillsborough.
Wednesday were in charge for much of the game but struggled to find a way through the Derby defence before Brunt latched on to a ball into the box after 63 minutes and then spun and rammed it home.
Derby suffered a further setback when Barnes brought down Graham Coughlan with a brutal challenge and was red carded for his second yellow.
But it spurred the visitors on and when Peschisolido arrived in the 77th minute he was booed on by the home fans. But he had the last laugh when he hit the equaliser after a goalmouth scramble.
Then in the dying seconds Howard powered through with a determined run before drilling home his shot from 15 yards.
Derby could have had an early lead only for a super save by Chris Adamson to deny Seth Johnson in the 14th minute when the former Leeds man lashed a shot from the edge of the box. Steve Howard then almost added the finishing touch to a Matt Oakley free-kick.
But the scare sparked Wednesday into life and a header from ex-Derby striker Marcus Tudgay was inches wide before Graham Coughlan headed wide.
And when an inch-perfect pass was threaded through by Chris Brunt, Frank Simek cut in from the right but smashed a rising shot over.
Brunt went close with another Wednesday effort after Deon Burton's deft flick had caught Derby on the hop and another Burton shot was blocked.
The breakthrough finally came for Wednesday after 63 minutes just two minutes after Sturrock had brought on striker Steve MacLean after injury in the hope of engineering a goal.
But when it came the goal was from Brunt with his second of the season. After a throw down the right, Derby failed to clear the ball in the box and Brunt saw his chance spinning and hitting his shot through the crowd for the lead.
But then came the sending off and Derby's amazing double to clinch all three points.