The 25-year-old Argentine overhauled Gerd Mueller’s tally of 85 – set in 1972 – to set a new benchmark which includes goals for club and country.
Messi set the new record by scoring twice against Real Betis on Sunday.
He fired in an angled shot after 16 minutes to equal the German’s record before adding a second with a low drive in the 25th minute to set the new mark.
Messi’s attempt to break Mueller’s record was in doubt after he was carried off on a stretcher during Barcelona’s Champions League group game draw with Benfica on Wednesday.
The forward feared he had seen the “last ball I’d touch for a long time because of the pain” but the left knee injury was not as bad as he thought and he started against Betis.