The midfield player hit a second-half equaliser for his side but was sent off in injury time after collecting his second yellow card for a foul.
Wednesday are planning to appeal against the one-match ban he is set to serve as they insist his second caution was undeserved.
But the play-off hopefuls are stuttering after five games without a win while Oldham took another step away from trouble at the other end of League One.
The Latics controlled the first half at Boundary Park and could have gone in front on just seven minutes as Kevin Betsy crossed to Chris Killen who lifted his shot over the bar from close range.
They pushed Wednesday on to the back foot and took the lead on 29 minutes through on-loan striker Luke Beckett.
The Yorkshireman ran on to a through ball from busy midfielder Neil Kilkenny and drove a superb shot inside the far post from 16 yards.
Oldham almost struck again through Killen before Beckett was unlucky to hit the crossbar from the edge of the box with a clever chip which beat the keeper.
Wednesday boss Paul Sturrock gave his side a rocket at the break and they came out fighting as James Quinn headed off target.
The leveller arrived on 54 minutes as John Paul McGovern found Whelan whose 20-yard effort seemed to take a deflection before beating Steve Mildenhall.
Quinn flicked another chance past the far post before Killen missed the target for Oldham.
There were six minutes of injury time during which Whelan's tackle on Kilkenny saw him get his marching orders.