The German worldwide suffered knee ligament damage after colliding with Kylian Mbappe in the 34th minute, however Kroos went on to play the entire 90 minutes which saw Los Blancos secure a two goal advantage over the Parisians after notching a 3-1 win, following a double from Cristiano Ronaldo and a strike from Marcelo.
RealMadrid will look to put their indifferent domestic form behind them when they travel to Real Betis on Sunday, live on Sky Sports Football.
A party atmosphere had gripped the Benito Villamarin stadium but locally-born Real captain Ramos punctured the mood by levelling with a towering header from a corner five minutes into the second half.
Real Madrid boss says he will fight till the end to stay at the Bernabeu.
Mandi had already headed one Joaquin corner wide but he was on target after 33 minutes, overpowering Casemiro in an aerial challenge to nod past Navas.
"Perhaps he will win it again and then fancy going off for a break".
The Frenchman has steered the Liga giants to eight trophies, including back-to-back Champions League titles, in the last two seasons since his appointment at the start of 2016.
And the goals continued to flow, Asensio on target with his second of the game to restore the Madrid lead, cushioning home a lovely first-time finish from Dani Carvajal's cutback after a brilliant run down the wing from the right-back.
Sergio Leon's late goal caused a few nerves at 4-3 before an injury-time fifth from substitute Karim Benzema.