In a game that finished 3-3 after extra time, Josh Murphy and Robert Glatzel struck either side of the interval for Cardiff before Omar Richards and substitute Andy Rinomhota forced another 30 minutes.
Murphy pounced on a Gabriel Osho mistake to poke home his second and restore Cardiff's lead, but Yakou Meite forced penalties four minutes from time.
Reading won the resulting shoot-out 4-1 as Garath McCleary, Osho, Jordan Obita and Sone Aluko gave the Royals a 100 per cent return from the spot and Cardiff's nerve buckled as Aden Flint and Will Vaulks missed.
This was the third meeting between the two clubs in 10 days, games more notable for incidents off the field than the action on it.
But the overriding mood this time was one of apathy with empty seats all around the Cardiff City Stadium.
Both sides made a raft of changes from their 1-1 draw in the Sky Bet Championship four days earlier – Cardiff seven and Reading six.
Reading midfielder John Swift fired wide inside five minutes, but Cardiff asked most of the questions in a first half which produced plenty of open football.
Murphy and Danny Ward fired over before the breakthrough came after 19 minutes, although it owed more to Reading carelessness than Cardiff creativity.
Charlie Adam gifted possession to Murphy, and the winger advanced to arrow home low into the corner of the net from 25 yards.
Ward should have instantly doubled the lead before Reading stirred in the closing stages of the first half.
Puscas headed wide when well placed and Meite forced Neil Etheridge into a point-blank stop with an audacious volleyed back-heel flick.
Cardiff doubled their lead after 54 minutes when Vaulks produced a peach of a pass with the outside of his foot to send Glatzel scampering through.
The big German has often been criticised for his finishing since arriving from Heidenheim last summer, but he showed excellent composure to slot home his fifth goal for Cardiff.
Reading refused to lie down and Etheridge produced a smart save to deny substitute Aluko before Richards halved the deficit with a bullet header after 69 minutes.
Rinomhota's stunning volley rewarded Reading's revival 11 minutes from time as the Cardiff goal came under late siege.
Etheridge produced superb stops to foil Rinomhota and Tyler Blackett and it looked as if Murphy had finally settled this trilogy with his fourth goal of the season.
But Meite rifled home four minutes from time – his third goal against Cardiff in 10 days – and Reading were just as deadly from 12 yards.