He notched his first after four minutes and his second on 77 as Real thumped their already-relegated opponents 8-1.
His double meant he moved two clear of the previous mark, which he jointly held with Real’s Hugo Sanchez and Athletic Bilbao striker Telmo Zarra.
Xabi Alonso’s free-kick to the far post was headed back across goal by Sergio Ramos and the unmarked Ronaldo was on hand to poke in the opening goal. His second came late in the game when he fired a long-range effort inside the far post.
Emmanuel Adebayor, whose loan spell from Manchester City is expiring, signed off with three goals, Karim Benzema bagged two and youth team player Joselu notched one at the end.
Ronaldo, who had scored nine goals in his previous three games heading into the final fixture, has scored 53 in all competitions for Madrid this season.
Messi was left out of the squad for champions Barcelona’s 3-1 league win over Malaga on Saturday. But the Argentine can add to his tally of 52 next Saturday when Barca face Manchester United in the Champions League final.