The Portuguese forward has rattled in 44 goals, four more than his record-breaking tally from last year which earned him a second European Golden Boot award, but is now two short of his great rival from Barcelona.
The man who replaced Ronaldo as World Player of the Year and retained it the last three years, Messi, scored a hat-trick in Barca's 4-1 home win over Malaga on Wednesday to move on to 46.
Ronaldo scored with a header against Athletic Bilbao helping Real seal a 3-0 away victory that secured them their 32nd league title on Wednesday, making amends for an earlier penalty miss.
An unusually timid effort from the 27-year-old, straight down the middle to be saved, was Ronaldo's first penalty miss in 12 attempts in La Liga.
It was his second failure from the spot since being denied in their semi-final shootout exit against Bayern Munich in the Champions League a week ago.
"What I really wanted was to win what I didn't have," Ronaldo told reporters when asked about Messi overhauling him in the league scoring chart.
"I have two Golden Boot awards at home. If I get a third, all well and good. But the important thing for me tonight was to win the league."
San Mames is traditionally a hostile stadium for Madrid and fans mocked Ronaldo for his penalty miss, prompting an angry reaction from the player after he scored his goal.
Ronaldo pointed at the club badge and at the football league logo on his white shirt, mouthing 'champions, champions' at the crowd.
After the final whistle, Ronaldo made a rude gesture to Bilbao defender Javi Martinez, who had been sent off in the second half, as the Spanish international appeared to complain about the way he was celebrating their triumph.
Members of the Real bench intervened to keep them apart.
Ronaldo's goals have helped Real smash the league scoring record of 107 set by themselves in the 1989-90 campaign and they have 115 with two matches still to play. Deposed champions Barcelona have also passed the previous record with 108.
The La Liga points record is also within reach for Jose Mourinho's side if they can win their remaining fixtures at Granada on Saturday and at home to Real Mallorca the following weekend.
Real have 94 from 36 matches, seven ahead of second-placed Barca, and could rack up 100.
Pep Guardiola's team amassed a record 99 points to win the second of his three league titles in the 2009-10 campaign. Real beat their club best tally with Manuel Pellegrini at the helm that year to finish second with 96.