That first-leg result flatters Los Merengues somewhat considering two of their three goals came in the last few minutes of their trip to Numancia, where Gareth Bale opened the scoring in his first start since September.
Real have since fallen further behind in their defence of La Liga's crown, having surrendered a late equaliser to draw 2-2 at Celta Vigo on Sunday, leaving them fourth in the standings and 16 points adrift of leaders Barcelona.
Numancia's hope of overturning a three-goal deficit in their visit to the European champions looks all but futile, particularly given Real are liable to pinpoint cup competitions as their best chance at silverware.
We take a look at Wednesday's second-leg meeting in Madrid, complete with live-stream and viewing information.
Date: Wednesday, January 10
Time: 8:30 p.m. GMT/3:30 p.m. ET
Venue: Estadio Santiago Bernabeu, Madrid
TV Info: Sky Sports (UK), beIN Sports 17 (U.S.)
Segunda Division side Numancia came away from Thursday's defeat to Real with some dignity intact regarding their performance, but it's inevitable they feel a sense of hopelessness looking at the scoreline.
Bale's penalty was all that separated the teams heading into the dying minutes of the clash, when Isco added a second spot-kick before Borja Mayoral's 91st-minute header settled the leg and seemingly the fixture.
As illustrated by Sunday's draw at Celta Vigo, however, Real haven't been their free-flowing selves of late—or this season, for that matter. The Guardian's Sid Lowe pointed to the fact four of their last five Copa goals have been penalties, suggesting the squad is struggling to craft and convert its usual amount of chances.
The closest Numancia came to getting on the scoreboard on home soil came via Inigo Perez, whose attempt to lob Kiko Casilla from halfway thudded off the crossbar, and they're bound to struggle more for chances in Madrid.
Real manager Zinedine Zidane has the option of fielding a strong side in Wednesday's second leg to ensure their progress, but it seems more likely a second string will line up with a three-goal cushion to their name.
Midfielder Marcos Llorente was particularly impressive at Numancia, while Zidane was pleased with the hour-long display of Bale, who stands a chance of starting again in midweek after netting twice in Vigo.
Per Spanish daily Marca, Zidane said of the Welshman: "This was the plan. He managed an hour and had no problems. We are happy and we will continue on this line. I think he'll play more and the idea is for him to have continuity."
Llorente could be another to benefit from another starting opportunity against second-tier Numancia, and Goal hailed his powerful display in the first leg, when he completed 95 percent of his attempted passes.
One who won't be present on the pitch Wednesday is Numancia midfielder Pape Maly Diamanka, who was shown a red card after two cautions on Thursday. Left-backs Adrian Ripa and Luis Valcarce are also doubts after suffering injuries in the first leg and missing Sunday's 2-2 draw at Cultural Leonesa.