Liverpool almost levelled immediately following the break, as Rio Ngumoha's low ball led to a dangerous opening for the Reds.
Real goalkeeper Alvaro Gonzalez attempted to clear and was caught short off his line with Michael Laffey's lofted, on-target effort from outside the box cleared away by the defence.
Kone-Doherty then saw a header brilliantly saved from a second Ngumoha cross as Gonzalez pushed away his close-range effort from underneath the crossbar.
In response, Misciur was again forced to punch away a swift shot at the end of a quick break from the visitors, denying Jesus Fortea this time, before Jaime Barroso headed wide at a corner.
Yanez also flashed a low shot wide of the mark from distance as the two teams continued to exchange opportunities.
Next, Josh Davidson's goalward low shot was deflected away by the retreating Madrid defence as another Ngumoha ball found its way through from the left.
Liverpool were applying stern pressure, though Real's threat on the break was clear, with Lucky providing another important challenge on the edge of the box to halt their latest counter-attack.
Misciur was also called into action once more to push away a shot from range, as was Gonzalez at the opposite end, but the Reds were unable to find a leveller in the final stages.
**Team**
Misciur, Esdaille (Young, 60), Pinnington, Lucky, Nallo, Laffey, Kone-Doherty, Davidson, Morrison, Nyoni, Ngumoha.
Unused subs: Hall, Bernard, O'Connor, Figueroa, Ahmed, Bradshaw, Sonni-Lambie, Pitt.
**Next up**
Liverpool's next Youth League contest comes on December 10 when they travel to face Girona in a 1pm GMT kick-off.
The fixture will take place at Camp de Futbol Municipal de Vidreres.