Chris Burke levelled moments before the break, before Whittingham and Ross McCormack wasted glorious chances.
Cardiff's Ross McCormack pulled one back on 19 minutes to score his 10th Championship goal of the season.
Should a Premier League club swoop for Ross McCormack, Pericard could be a possible replacement for the Scotsman.
But a header from Ross McCormack restored parity before Nunez tapped in to win it for the Championship side.
Peter Ramage denied Ross McCormack before Peter Whittingham sliced Bothroyd's downward header wide.
The Bluebirds almost had a second in as many minutes when last season's top scorer Ross McCormack toepoked just wide.
Among those omitted from the squad were Celtic defender Stephen McManus, who is on loan at Middlesbrough, and Cardiff striker Ross McCormack.
They have people like Chopra and Peter Whittingham, as well as Ross McCormack and Jay Bothroyd, so they are a real threat at that level.
Motherwell were fired up early in the second half and only a double block denied Clarkson and Ross McCormack from close range.
Fielding was equal to Ross McCormack's 35-yard effort while the Rams stopper also denied Snodgrass and beat away a drive from Danny Pugh.
Chopra, 24, is back at the Bluebirds until January to help plug the gaps created by injuries to Jay Bothroyd and Ross McCormack.
Goals from Robert Snodgrass, Ross McCormack and Luciano Becchio saw Leeds defeat 10-man Ipswich and move to within a point of the play-off zone.
While Bothroyd's knee injury looks more serious as he was forced off half way through the first half to be replaced by Ross McCormack.
"We've made our move, we've put a bid in for Ross McCormack but the bid has been rejected, " Brown told the Hull Daily Mail.
Smith hopes to emulate former team-mates Ross McCormack, Charlie Adam and Chris Burke, who have all enjoyed success in the English Championship since leaving Rangers.
Meanwhile, Malpas reported that striker Ross McCormack, missing for a number of months following a virus, played the bulk of the closed-doors game, scoring twice.
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Rangers' Allan McGregor was tested when Steve McGarry's cross found the diving head of Ross McCormack 10 yards out and the ball bounced clear off the goalkeeper's knees.
Gordon received noisy backing from the Hampden crowd, who were cheering his name throughout the win, which was secured thanks to goals from Ross McCormack and Steven Fletcher.
But Cardiff pulled a goal back on 19 minutes after a Miguel Comminges overlap and cross from the left was brought down superbly by Ross McCormack, lurking on the penalty spot.
He made an almost instant impact as he won Cardiff a penalty after being fouled by Valencia's Hedwiges Maduro but Ross McCormack missed the spot-kick as the Spanish giants earned the pre-season win.
Chelsea beat Preston North End at Deepdale 2-0 to secure a fifth round clash while injury-hit Cardiff needed stoppage time goals from Chris Burke and Ross McCormack to beat Championship rivals Leicester City.
Ross McCormack has made a good start to life at Cardiff and could win a place among the forwards, while Wolves striker Chris Iwelumo has netted eight goals in seven matches but has landed an untimely suspension.
The 22-year-old midfielder, key centre-back Roger Johnson, top scorer Ross McCormack and full-back Kevin McNaughton will attract attention from big clubs after Cardiff failed in their promotion quest despite being in the top six virtually every week since October.
The lead took the sting out of the game and Cardiff tried to get themselves back into it with Ross McCormack, back for his first start in almost three months for suspended top-scorer Michael Chopra, lifting the ball over the bar from the edge of the box.
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