The 22-year-old was forced off in the 22nd minute of the encounter after rupturing his knee ligament and was subsequently hauled off.
On Monday, the club confirmed that the former Atletico Madrid youngster had a successful surgery and wish him a quick recovery.
"Amath Ndiaye has been successfully operated on at the Cemtro Clinic by doctors Eulogio Martín and Manuel Leyes for a ruptured anterior cruciate ligament of his right knee," read a statement from the club website.
"The healing period is estimated around six months. We wish him a speedy recovery, and to be able to see him as soon as possible on the playing field."
This season, Ndiaye has made 15 league appearances for the Deep Blues, scoring once to help them to the eight