"Congratulations Madrid," Puyol wrote on Twitter after the final whistle on Saturday. "Four Champions Leagues in five years with one of the best Barcelona sides in history... we must reflect on our priorities.
"You can never chuck La Liga away, but in the cup you have to play those that don't play regularly and be at your best for the Champions League. That said, I think Barca had a great season."
With Barcelona lifting the domestic double, Real success in the European Cup competition has overshadowed their recent success and Puyol has now questioned certain aspects of his former side.
With four successive Copa del Rey titles, the former Spain and Blaugrana captain feels the club's priorities over what's important needs to be assessed.
While Puyol stopped short to claim he was having a dig at Barca and head coach Ernesto Valverde by congratulating Los Blancos on Twitter he insists the Blaugrana hold a better side than their fierce rivals.
"What I hoped to do was to invite some reflection," Puyol told La Vanguardia. "I am convinced that [Barca] have a better team than Madrid and yet they've won four Champions Leagues in five years.
"I think the solution is to not make mistakes with your priorities. [Barca are] losing an opportunity and it angers me as a Barca fan.
"The posts shouldn't be interpreted as a knock to the club or to Valverde," he added. "The double has a lot of merit -- I know how hard it is to win that.
"But we have a great team and we have Leo [Messi]. The Champions League is played on a global level and it also contributes to the Ballon d'Or.
"I have no doubt who the best footballer in the world is but you must take advantage of [Messi's] talent in La Liga and in Europe."