Wanderers, watched by potential new owner Dean Holdsworth and who finished with 10-men, twice came from behind before Pilkington struck to leave the home side rooted to the foot of the table.
Tony Watt and Scott Malone twice put Russell Slade's side in front but goals from Gary Madine and Dorian Dervite brought the Trotters back into contention before Pilkington's late intervention.
Appalling weather conditions simply summed up the storm clouds hovering over the famous Lancashire club. The torrential rain and howling wind also ensured a pre-match plea from fans to fellow supporters to #fillthemacron fell short of expectation with only 13,241 eventually turning up.
So, the mood hardly improved when Cardiff went ahead against the run of play after 11 minutes. Ex-Celtic striker Watt, who made his Cardiff debut a week earlier against Burnley, took advantage of static defending from Dervite to cut into the penalty area before shooting low past Ben Amos.
It was only on loan Watt's fourth goal of the campaign and his first since netting for Charlton on August 15.
But five minutes later Wanderers levelled just as heads began to drop. There appeared little danger as Madine picked up the ball on the Wanderers left. But like Watt he turned inside before curling an angled right foot drive into the bottom of David Marshall's net.
Neil Danns, scorer of Bolton's equaliser against Brentford last Monday, had the City captain scrambling minutes later with a spectacular 35-yarder.
Wanderers skipper Darren Pratley should have scored from six yards out following a Dean Moxey cut back. Instead, his shot hit a Cardiff defender and cannoned onto the crossbar.
So, it was against the run of play when the Bluebirds restored their lead after 53 minutes. Scott Malone prodded the ball past Amos after the ex United keeper saved the initial shot.
Madine fluffed a close range header to make it 2-2 while Watt netted again after 63 minutes only to be ruled offside.
But Wanderers kept pressing and equalised for a second time through Dervite's first goal for the club after 71 minutes. The former Charlton defender stabbed the ball past Marshall to set-up a frantic finale.
And 10 minutes from time beleaguered Bolton conceded to Pilkington's volley before Spanish defender Jose Manuel Casado was sent off for his second bookable offence.