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Gary McSheffrey replied in style 40 minutes later, pouncing on Mark Hudson's poor pass near half-way to beat Kevin McNaughton and hit home.
But Bothroyd hit the net after Chris Burke's late run down the left.
Bothroyd's every touch was greeted by boos from the home fans, but he left the field a winner as the Bluebirds cut QPR's lead at the top to two points after the London club drew 0-0 at Swansea.
The home fans reserved most of their venom for Cardiff captain Craig Bellamy, another former Coventry player.
But having been on top for most of the opening period the home side had Hudson's mistake and McSheffrey's goal-scoring instincts to thank for bringing them back into the contest.
McSheffrey left Cardiff keeper Tom Heaton with no chance as he hit home after easily seeing off McNaughton.
The Sky Blues also had the better of the exchanges after the restart as Sammy Clingan and Lee Carsley dominated in midfield.
But Heaton denied Aron Gunnersson and Coventry kept lively Bellamy at bay at the other end.
The Bluebirds had threatened from the opening whistle and Chopra was on the point of tapping home from Whittingham's low cross when Turner bundled him over.
Bellamy, Chopra, Whittingham and Gabor Gyepes also threatened as the hosts defended for long periods of the opening half.
But having been on top for so long, Dave Jones' side found themselves starting from scratch as defender Hudson's series of poor passes eventually gave McSheffrey his chance.
That moment handed the initiative to Coventry, but Cardiff regained supremacy as the game wore on.
And when Burke at last broke free down the left to deliver a Bothroyd his chance, the striker took it, darting in from the far post to the front and sending the ball into the back of the net with the outside of his left foot.
Burke then produced a second successful run on the left, but was unable to hit home with his final touch.
Source: BBC Sport
Other reports
Cardiff Official website
Coventry Official website
ESPN Soccernet