Despite missing a penalty and forging ahead, Boro succumbed to a stoppage time winner having played against ten men for fifty five minutes.
Coach Paul Jenkins made two changes to the eleven beaten by Sunderland on Monday.
With Alex Baptiste and Rhys Williams having linked up with the first team training camp in Marbella, Matthew Elsdon and Alex Pattison were restored to the starting eleven.
Liverpool named a strong side full of Premier League experience including Adam Bogdan, Jon Flanagan, Jose Enrique and Sheyi Ojo.
Boro survived a scare in the opening minutes. Liverpool attacked at pace down their left with Sheyi Ojo's fierce cross almost turned into his own net by Robbie Tinkler who snatched at his attempted clearance.
Boro came more into the game with Jordan Jones proving a central figure.
His driving run into the box resulted in a penalty after his surge was abruptly halted by Joe Maguire's mistimed challenge. Jones picked himself up to take the spot kick himself but keeper Adam Bogdan guessed correctly making a smart save dropping to his left
The penalty miss didn't detract from Middlesbrough's focus as they forged ahead in the 34th minute.
Liverpool defender Cameron Brannagan was red carded for a body check on Jones just outside the penalty area.
From a central position Arnel Jakupovic drove the free kick emphatically past a five man wall and keeper Adam Bogdan
Half Time. Liverpool 0 Middlesbrough 1
Despite being at a numerical disadvantage Liverpool's desire after the break was conspicuous.
Alex O'Hanlon and Ojo came close before Sheyi Ojo levelled in the 53rd minute, seeing his low angled shot from the left of the box drift under Joe Fryer's dive.
Boro eventually quelled the Liverpool attack and fashioned two chances for a winner.
Hungarian keeper Adam Bogdan displayed his international pedigree keeping out Callum Cooke who showed great composure in the box and also blocking Josef Wheatley's attempt.
Liverpool's winner arrived three minutes into stoppage time. Callum Johnson tripped substitute Brooks Lennon in the box, allowing Sheyi Ojo the opportunity from twelve yards which he took emphatically condemning Boro to their second defeat in four days.
Bogdan; Flanagan, Enrique, Ilori, Maguire, Brannagan (Capt.), McLaughlin (Virtue 37(Gomes 78)), O'Hanlon, Sinclair (Lennon 91), Kent, Ojo. Subs: Firth, Hart.
Fryer; Johnson, Eldson, Burn (capt.), Kitching, Tinkler (Wheatley 57), Chapman (McAloon 73), Pattison, Jakupovic, Cooke, Jones. Subs: James (gk); Jowers, McGinley.