Competing in the Copa del Rey quarter-finals for just the second time in their history, Los Pepineros came flying out the blocks early on, with Diego Garcia seeing a sharp effort thwarted by Andriy Lunin and Valentin Rosier blazing wastefully over from close range.
Grateful to still be on level terms, Real found a breakthrough against the run of play in the 18th minute when Luka Modric tucked a brilliant finish beyond Juan Soriano after good work from Rodrygo out wide.
Armed with the momentum, the visitors doubled their lead just seven minutes later through Endrick, who pounced on a loose ball in the box to sweep home from eight yards.
Leganes refused to lie down without a fight, however, and the hosts were given a golden opportunity to halve the deficit when Jacobo Ramon was penalised for blocking Juan Cruz’s goalbound effort with his hand.
Cruz assumed the responsibility from the spot and finished confidently into the bottom corner for his first goal since the start of November.
Vinicius Junior was introduced by Carlo Ancelotti at the break and the Brazilian nearly had an immediate impact when his powerful effort was denied by Soriano.
Federico Valverde and Endrick wasted further chances for Real, and the visitors’ profligacy was soon punished, as Cruz latched onto Darko Brasanac’s cut-back and saw a low strike deflected beyond a helpless Lunin to draw Leganes level.
That set up a fascinating final half-hour, with Real going agonisingly close to regaining the lead when Brahim Diaz clipped a delicate effort onto the bar.
The hosts remained a threat at the other end as Dani Raba’s drilled strike from range was thwarted by Lunin, but it was Los Blancos who found the all-important moment of quality deep into stoppage time.
Diaz’s inviting delivery was perfect for substitute Garcia, who directed a brilliant header into the corner for his first senior goal for the club, sealing Real’s spot in the final four in dramatic fashion.