Cristiano Ronaldo popped up with the winner for Jose Mourinho's men on 73 minutes, just moments after Blaugrana substitute Alexis Sanchez had cancelled out Sami Khedira's first-half opener.
However, Busquets felt that the visitors' victory, which has all but secured the Liga title, was undeserved because of their perceived ultra-defensive approach to the game.
"We did what we could, we were faithful to our style of play and I believe that we played better than they did," the Spain international is quoted as saying by his club's official website.
“Real Madrid closed themselves off at the back the whole game. They didn’t play at all. They just looked for the counter, but sometimes football is like that.
“They did very little to win the game. It’s a bit unjust, I hope Tuesday isn’t like today ..."
Busquets was, of course, alluding to the midweek meeting with Champions League rivals Chelsea. The Blaugrana dominated the first leg of their semi-final tie at Stamford Bridge but came out on the wrong side of a 1-0 scoreline.
Consequently, the midfielder is now desperately hoping that Barca's luck changes on Tuesday night.
“We have to face the game like a final," the World Cup winner reasoned. "We have to overturn the adverse result.
"I hope what happened today [against Madrid] and against Chelsea [last week] doesn’t happen again."
Indeed, Busquets insisted that even though Barca have now fallen out of contention in the battle for the Liga title and face an onerous task in trying to reach the Champions League final, he remains confident that they will not end their campaign without any silverware.
“We gave it our all [against Madrid] and we’ll keep on trying until the end," he declared. "It’s a pleasure to watch us play and we’ll stay united. I believe that we’ll have a good end to the season."
Barcelona's mouth-watering match-up with Chelsea kicks off at 20.45 at Camp Nou.