The epic shootout, which was only settled when Boro’s Albert Adomah missed with the 30th spot-kick, equalled the British record for the highest-scoring post-match contest, set over three years ago when Dagenham and Redbridge edged past Leyton Orient in a Football League Trophy tie.
After failures from Patrick Bamford and Raheem Sterling, the next 20 penalties in sudden death were all converted – until Adomah sent his effort wide.
Teenage midfielder Jordan Rossiter, a product of the Anfield academy system, had needed less than 10 minutes of normal time to make a significant contribution on his senior debut, but Adam Reach equalised for Boro to send the match past the 90-minute mark.
Suso stepped off the bench to put the hosts back in front in the second half of extra-time, but a moment of madness from Kolo Toure in the dying stages presented Bamford with an opportunity to level from the spot, resulting in the shootout which eventually put Liverpool into the fourth-round draw.
Early on in the match, a breakdown in communication between Boro goalkeeper Jamal Blackman and defender Kenneth Omeruo resulted in the pair being caught out of position and, despite Blackman blocking from Rickie Lambert, Anfield academy product Rossiter took full advantage to guide the ball into the back of the net from 35 yards out.
Parity was restored just past the hour mark when Grant Leadbitter swung over a dangerous free-kick and Reach displayed the greater desire in a battle with Jose Enrique to nod in from close range.
It took until the 109th minute for Brendan Rodgers’ side to break through for a second time, with neat play from Adam Lallana leading to a scramble inside the Boro box which allowed Suso to drill low through a crowd of bodies on the line.
That looked like being enough, but a clumsy challenge from Toure on Bamford allowed the latter – on loan from Chelsea – to calmly stroke home from 12 yards in stoppage-time.
The 21-year-old then saw his effort in the resulting shoot-out saved by Simon Mignolet, but Sterling also failed from 12 yards and with the tie taken deep into sudden death, Adomah ended up being the fall guy as he blazed wide with the 30th kick of an astonishing contest.
Rodgers suggested in the build-up to the game that the Liverpool shirt being “heavy” for incoming players to wear due to the pressure of expectation had been a contributing factor to the Reds’ slow start to the season.
But there was little evidence of 17-year-old midfielder Rossiter experiencing such a feeling as his first senior appearance began with a bang.
Sterling chased a long pass over the top which Omeruo and Blackman got in a mess trying to deal with, and the latter then managed to get in the way of a follow-up shot by Lambert, the captain for the night making his first Liverpool start.
The loose ball fell to Rossiter, who caught out Blackman – a debutant himself, also on loan from Chelsea – with a calm, first-time shot into the net.
That the Liverpool youngster should appear so immediately comfortable in the team is perhaps unsurprising – he has been with the club’s academy since under-six level.
But there seemed to be a malaise creeping back in for Rodgers’ team, which showed seven changes from Saturday’s 3-1 loss at West Ham, as the first half went on.
After Lallana struck wide in the 25th minute, the visitors started to show some threat, with Kike sending a volley over via a Lambert deflection and Mignolet then doing well to push away a powerful Lee Tomlin strike.
Boro kept pressing as the second half got under way, with Tomlin firing wide.
And their perseverance was duly rewarded when Leadbitter swung in a free-kick from just outside the corner of the area and hesitant Liverpool defending saw Reach get to the ball ahead of Enrique and glance in.
Sterling looked to reply but could only shoot at Blackman, and Reach was then unable to divert another headed effort on target.
Liverpool had penalty claims turned down when Lallana went to ground under the attentions of Ryan Fredericks, and after a further appeal for a handball just outside the box equally was also ignored, Lazar Markovic’s through-ball to Sterling was intercepted by a last-ditch tackle.
Rodgers sent on Mario Balotelli for Lambert and Mignolet then pulled off a fine diving save to keep out a Clayton shot that that looked bound for the net.
Boro sensed the upset was on and Clayton almost sealed it with five minutes of normal time remaining when he latched on to a superb pass from Tomlin and shot against the woodwork.
At the other end, Balotelli scuffed wide as he lost his footing, and the hosts’ penalty cries went unheeded once again in stoppage time as Boro’s former Liverpool defender Daniel Ayala appeared to handle while trying to clear a cross.
The Reds showed little conviction with their finishing in extra-time until the ball broke to Suso – who had come on for Markovic – from a goalmouth scramble and the Spaniard slotted in.
Liverpool looked to be almost over the line, but Boro were not finished and they found themselves back in the game at the death when Bamford, clumsily brought down by Toure, put away the resulting penalty.
That set up a shoot-out which will stay in the memory – but will not be remembered with any fondness by Adomah.