Goals from Gareth Bale and Cristiano Ronaldo on either side of half-time looked to have ensured Los Blancos a victory, however a goal 20 minutes from time by Giovani Dos Santos saved El Submarino Amarillo from their blushes.
And the 48-year-old tactician believes that his team's fortunes would've been different had it been on another day.
"I want to thank the players, who are playing and working in a commendable fashion and were superior to Real Madrid, although it was a shame that after so much work and effort, we could not succeed in bringing back a deserved victory," he told reporters.
"If we had success and we had not met a goalie like the one Madrid had today, after half an hour we would've reached a three-goal lead.
"Also, in the second half we could've returned to control things and led, but we did not, while they took their chances with a counterattack."
Despite the disappointment, Marcelino reiterated the club's desire for success, echoing the need to stick the club's objectives.
"This (result) does not change our goal and we must follow step by step in order to add those 42 points, ensuring that we will stay (in the league) as soon as possible".
Villareal are currently placed third in the league and are preparing for their next match against Celta Vigo