The two clubs will meet again at Santiago Bernabeu this weekend, with nine points between them in the La Liga table.
Barca are on course to win a domestic double this term after a 3-0 Copa del Rey semi-final triumph over their arch-rivals in midweek, while Madrid are in danger finishing the season without a trophy.
Ernesto Valverde's side have once again relied on the brilliance of Messi to spearhead their hunt for silverware, with the club captain scoring 33 goals in 32 matches across all competitions.
The 31-year-old superstar is a five-time Ballon d'Or winner and has been described by many fans and experts as the greatest player in the history of the game.
Even as Messi approaches the twilight years of his career, he is showing no signs of slowing down and Morientes believes that it is a handicap for Madrid to come up against Barca with him leading their team.
"Barcelona have always been a dangerous team, a very difficult rival regardless of the era, " Morientes began.
"El Clasico has always been special. In our day it was a tough game, but today it’s even tougher because they have Lionel Messi.
"He’s a player that we’ll look back on years from now as someone who was on a different level, special.
"I’ve been lucky – or unlucky – enough to face him and I know what he’s capable of.
"He has the ability to break open a game, he’s the difference in an even game. Having him on the opposing team is a big handicap."
Morientes played as a centre-forward for Real Madrid between 1997 and 2005, winning three Champions League titles and one Liga crown.
In 242 appearances for the Blancos, the Spaniard scored an impressive 91 goals, contributing his fair share during titanic battles against Barcelona.
Looking back on his eight-year spell at the Bernabeu, Morientes went on to discuss his recollection of being involved in a Clasico for the first time, stating he was 'lucky' to experience the fixture at such an early stage of his career.
"My most special Clasico was my first," Morientes continued.
"When you play for Real Madrid you want to play every game, obviously. But you always know when El Clasico comes around when it’s Real Madrid vs Barcelona.
"I was lucky enough to play it very early on in my career. They’re games you don’t forget.
"I played a lot more over the years, and had already played big games for Real Zaragoza and Albacete, but that first Clasico was unforgettable.
"I was even lucky enough to score, so all good!"