Barcelona claimed a 1-0 first-half lead thanks Ivan Rakitic's delicate finish in the 26th minute, but Mourinho felt the match lacked the customary intensity of European football's fiercest rivalry.
Ramos caught Messi with a flailing arm, leaving the Barcelona superstar prone on the turf before he confronted his opponent and protested to the referee – Alberto Undiano Mallenco, who decided no action was necessary.
Speaking in his capacity as a pundit on beIN SPORTS, former Madrid boss Jose Mourinho suggested Ramos knew exactly what he was doing.
"I think in the first half, both teams when they had the ball, they did not hurt the opponent too much," he said.
"There was no intensity on the defensive actions, with everybody playing in a low-medium block.
"It was not the temperature of a derby, of a Clasico that can settle the title.
"I think Sergio Ramos' action probably is coming from a player that knows the game has to change.
"And probably he does it with the intention of creating a different temperature for the second half, because the game until then was really soft, in my opinion."
Ramos is no stranger to on-field controversy in high-profile matches and was the subject of prolonged scrutiny after his tangle with Mohamed Salah during last season's Champions League final left Liverpool's star forward with an injured shoulder before Madrid secured a 3-1 win.
UEFA has banned the 32 year-old for two Champions League games after it ruled he deliberately got himself booked during last month's first-leg win over Ajax in the last 16 in order to trigger a suspension.