Splashing through puddles that made playing a passing game next to impossible, Real ground out the victory that maintained their eight-point gap behind leaders Barcelona thanks to a late winner off the bench from 20-year-old forward Alvaro Morata, his first goal for the club.
"Result from the Spanish waterpolo League: Levante - Real 1:2," playmaker Mesut Ozil wrote sarcastically on his Twitter feed.
Ronaldo suffered a nasty gash above his left eye after he was caught by David Navarro's elbow early in the game but after being patched up he played on and scored Real's 21st-minute opener before being replaced by Raul Albiol at the break.
Mourinho said the blow, which left one side of Ronaldo's face covered with blood, had affected his Portuguese compatriot's vision and he was due to have tests on his return to the Spanish capital.
It was unclear whether he would be able to join up with the Portugal squad on Monday for their trip to play a friendly against Gabon on Wednesday.
Mourinho was happy to come away from Valencia relatively unscathed and it was the first time his Real side have beaten Levante there since he arrived from Inter Milan in 2010.
The champions, whose title defence got off to an erratic start, are third on 23 points, five behind Atletico Madrid in second and eight behind unbeaten Barca.
"It was a difficult match for everyone," Mourinho said.
"We adapted to the conditions and it was an honest battle between serious people who gave everything in search of a result," he added.
"The team had to draw on all its character and strength and we were deserved winners. I had never won here and they are three extremely important points."
Mourinho even suggested some may have enjoyed the spectacle of the players trying to cope with the ball holding up on the sodden surface.
"For all of us who have played football, whether well or badly, it was a party when you played in the rain as a kid and I think that in their way, people like it," he said.
"The more technical side and the referee have more problems, the fans too because it's cold and raining. That's part of football too and you have to adapt."
Spanish media reported that Levante captain Sergio Ballesteros had clashed with Real defender Pepe near the dressing rooms after the game and police officers had to intervene to calm down officials and players from both teams.