Messi put Barca 2-1 up just before halftime from the penalty spot and then latched onto a pass from compatriot Javier Mascherano to slam the ball beyond Diego Alves' near post and hit his 25th league goal of the campaign.
In addition, he has scored 11 times in the Champions League, four in the King's Cup and one in the Spanish Super Cup - with his tally currently standing at 41.
Messi first scored 40 goals in a single campaign in the 2009/10 season and has repeated that feat every season since.
"It's amazing, he's broken every record and will continue to break more," Luis Enrique told reporters.
How marvellous it is to enjoy Messi, no-one can touch his numbers, it's impossible for anyone to do what he has done apart from him. We'll miss him when he's gone.
Read the full article on eurosport.co.uk: Enrique and Pique can't bear to think of Barca without Messi