It sparked fury from home fans as they chanted taunts at McCarthy who turned and faced them with his arms raised in an ironic cheer.
And with Wednesday stretched, Keogh rammed home an angled shot after McIndoe and Jay Bothroyd combined.
Wednesday gave Wolves a couple of early frights as they set the early pace. Deon Burton teed up Glenn Whelan who blazed his shot over from 25 yards.
And when Chris Brunt fed Peter Gilbert the left back's cross found Marcus Tudgay at the far post but his hurried volley flew wide.
Wolves looked off colour, but Jamie Clapham's long ball aimed for Keogh caused problems when Richard Wood headed back and keeper Iain Turner struggled to hold it as he darted out.
But Wednesday, buoyed by their 2-0 midweek victory over Colchester, forced themselves in front after 21 minutes when Burton claimed his ninth goal of the season.
Simek's throw was flicked on Lee Bullen and Burton pounced on the awkward bouncing ball poking in his shot as Wolves dithered in the six-yard box.
Four minutes later Wednesday were denied a second when midfielder Chris Brunt produced a fabulous dipping free-kick from 30 yards which hit the bar after evading Matt Murray's outstretched fingertips.
But on the break Wolves could have been level in 34 minutes when Wednesday were caught out by a long ball that triggered a sprint from Keogh as keeper Turner raced off his line.
Keogh aimed a low shot for the open goal but somehow centre-back Wood managed to race back and hook the ball off the line as the home fans held their breath.
But the goal-saving intervention only delayed Wolves for a minute, 60 seconds later they were level when Michael Kightly produced an accurate cross for McIndoe to head in his fifth of the campaign.
Jan Budtz, on loan from Doncaster, had his first touch when MacLean played a one-two with Burton and crashed a low shot from the edge of the box inside the post leaving Budtz to have his touch - collecting the ball from the back of the net.
But 11 minutes from the end Simek was red-carded and Wednesday finally cracked when Keogh slammed home a low shot two minutes from the end.