Doncaster defender Gareth Roberts appeared to have halted free-scoring Cardiff's recent surge with a deserved second-half equaliser after home striker Michael Chopra had clinically despatched his 16th goal of the season in the ninth minute.
The Bluebirds had fired 10 goals in their previous two matches, including their 6-0 rout at Bristol City in midweek, but played second fiddle for long periods against Sean O'Driscoll's classy Rovers, who deserved at least a share of the points.
Whittingham had already fired a 25-yard shot over the crossbar for Cardiff when his raking pass dropped perfectly for Chopra, who raced into the penalty area and planted a low right-footed shot across Doncaster goalkeeper Neil Sullivan and into the far corner.
Bothroyd flashed a shot over the crossbar soon after, but Doncaster fired a warning in the 19th minute when James Coppinger crossed for Billy Sharp to head inches off target.
Chopra forced Sullivan into a fine save with his feet as the ball broke in the centre of the area and at the other end Rovers skipper Brian Stock tried his luck with a dipping 25-yard effort that flew over.
Chopra dragged another effort wide midway through the first half, but Doncaster shaded possession and although Ross McCormack headed wide for City from Chris Burke's crss, Bluebirds defender Gabor Gyepes was at full stretch when he lunged to block Sharp's goalbound shot from the edge of the area.
Doncaster almost drew level two minutes after the restart when Coppinger's angled shot was turned round the post by Cardiff goalkeeper David Marshall, but the visitors were not to be denied in the 65th minute.
John Oster crossed from the left and Roberts cut in on the left side of the penalty area and lashed a low left-footed shot into the bottom corner for a deserved equaliser.
Rovers striker Dean Shiels saw his 12-yard shot blocked by Cardiff defender Anthony Gerrard as the visitors chased a second, while Cardiff responded from long distance, with McCormack's 30-yard drive held by Sullivan.
Doncaster continued to press and looked the more likely to win it as the game entered the final quarter.
Coppger's brilliant overhead kick required a smart save from Marshall and Bluebirds manager Dave Jones sent on Kevin McNaughton and Solomon Taiwo for Burke and Mark Kennedy in a bid to shake-up his side.
Dean Shiels then drilled a 20-yard shot just over the target for the visitors, who looked muchthe better side as their fluent passing style left the home side chasing shadows.
But Cardiff mounted one last advance and Bothroyd latched onto Whittingham's last-gasp cross to keep the Welshmen in fourth place in the table.