His 20-yard strike appeared to be comfortably heading into the grasp of home keeper Josh Lillis until it took a wicked bounce in front of him and looped into the goal.
It was just reward for Cardiff's second-half showing, though, and helped them secure their 23rd point on the road this season.
After putting in their best performance of the campaign to beat Derby 4-1 last weekend, Scunthorpe were eager to transfer that form into this clash and began causing their visitors problems from the off.
Paul Hayes was the first to look dangerous as he flashed a shot just wide, while Garry Thompson, who scored twice against Derby, also went close to opening the scoring.
And they did not have to wait too long to turn their dominance into a goal as O'Connor produced a moment of class 15 minutes in.
A handball from Anthony Gerrard gifted the Iron a free-kick on the edge of Cardiff's area and Northern Ireland international O'Connor whipped a fine effort around the wall for his second goal of the season.
Cardiff then rallied, with Michael Chopra registering a couple of tame efforts on goal, while Chris Burke's drive drew a smart save out of Lillis.
Gary Hooper then threatened for Scunthorpe with a fizzing strike that was blocked by Gerrard, while at the other end Jay Bothroyd saw two efforts in the space of a minute kept out by the home defence.
The chances continued to present themselves to both sides, with Hayes and Chopra again trying their luck, but neither were able to find the net before half-time.
The start of the second period was considerably less frantic than the first, with City keeper David Marshall's smart handling of O'Connor's wicked cross the highlight.
Bothroyd continued to be frustrated in his quest for a goal and saw his long-range shot flash wide of the post, before Gerrard sent a free header over the bar from a Whittingham corner.
Frustratingly for City boss Dave Jones, the better of his side's opportunities continued to fall to Gerrard, who was soon sending another header over the frame of the goal, this time from six yards out.
O'Connor could have finished things for Scunthorpe but he could only float an effort wide with 15 minutes to go, before Gerrard redeemed himself somewhat by hooking Hooper's deft flick off the line.
And that intervention proved to be a vital one as Whittingham levelled.
Ross McCormack could have won it for Cardiff, only for his 25-yard effort to be clawed away by Lillis.