Lewis was the linesman who failed to spot Pedro Mendes' 'goal' at Old Trafford in 2005, when the then Spurs midfielder's long-range strike was two feet over the line before Roy Carroll scooped it away..
Lewis looked on in the 20th minute as Chris Brunt crossed, keeper Luke McCormick jumped to collect but dropped the ball as he was challenged by Deon Burton and, as the Plymouth players waited for the whistle, Steve MacLean almost apologetically stabbed the ball over the line.
Plymouth, who face Watford in their cup clash on Sunday, showed eight changes from the side which drew with Stoke on Saturday.
And they were in trouble after three minutes when Jermaine Johnson found space on the right flank as whipped the ball across the face of goal. MacLean, in for the suspended Marcus Tudgay, slammed in a low strike which was cleared off the line by Paul Connolly.
Plymouth, still harbouring hopes of a top-six finish, were foiled by Wednesday's on-loan keeper Iain Turner, who produced a spectacular stop to turn striker Bojan Djordjic's deceptive shot on the turn around the post.
Dangerman Johnson drilled a long-range strike from 25 yards over before the Hillsborough side snatched the lead in bizarre fashion.
Brunt pumped over a hopeful cross from the left flank, keeper McCormick jumped to collect but lost his footing and dropped the ball as he fell over Burton. Referee Lewis allowed play to continue as MacLean stabbed it over the line.
Plymouth were almost level in the 35th minute as David Norris' corner evaded the Wednesday defence and centre-back Hasney Aljofree thumped a fierce header against the crossbar.
Brunt was foiled by the Plymouth keeper minutes before the interval when his vicious in-swinging corner was plucked from under the bar by McCormick, before Johnson saw his deflected strike flash inches over the top.
Plymouth were level in then 56th minute when the hard-working Dan Gosling rifled in a right-foot shot from 16 yards after neat work by striker Rory Fallon.
Defender Richard Wood, back in the side after being sidelined through injury for 12 months, should have put the Sheffield side ahead again when he beat the offside trap but the big centre-back blasted the ball high over the target.
MacLean, battling to keep his place in the side, went close minutes later with a stinging shot from 25 yards but the ball flashed inches wide of the far post with McCormick scrambling across his line.