Following the interval, the Reds picked up the pressure once again, Wright first producing a header to draw another save, while Morrison fizzed a shot over the bar.
The match continued in competitive fashion as Cooper saved from Morrison again, before a one-two between substitute Figueroa and Kone-Doherty saw a low strike fly inches wide.
At the other end, Stoke were proving a threat on the counter, with Favour Fawunmi responding with an effort past the post after cutting in from the left flank.
However, with four minutes remaining Liverpool finally grabbed the second goal they had threatened throughout.
It was Figueroa on target, converting from close in after a ball from Morrison found Kone-Doherty, before his resulting shot was blocked and fell into his teammate’s path.
In the closing stages, goalkeeper Armin Pecsi produced a stretching save to deny the advances of Japhet Matondo, while Lucas Pitt first blocked well and then cleared off the line to ensure the spoils were claimed.
Liverpool U21s: Pecsi, Ramsay (Miles, 73), Pinnington, Lucky, Pitt, Trueman (Davidson, 55), Morrison, Pilling, Wright (Figueroa, 58), Laffey, Kone-Doherty.
Unused subs: Hall, Airoboma.