The Argentine failed to find the back of the net as FC Barcelona lost three crucial points at Malaga, but did score a brace in their midweek win over Sevilla.
At the top, Edinson Cavani, who did not have a midweek league game, added another two goals to his tally on Sunday to pull away from Messi, and now leads with 29 goals.
Robert Lewandowski overtook Pierre-Emerick Aubameyang – the only African among the top 10 – with his brace in Bayern Munich's 4-1 victory over Borussia Dortmund, when both Bundesliga strikers met directly on Saturday.
Edin Dzeko, Andrea Belotti and Alexandre Lacazette were also on the scoresheet over the weekend, while Romelu Lukaku widened his gap atop of the Premier League top scorers list.
Ronaldo, meanwhile, lost further ground in the Golden Boot race after failing to score in his past three La Liga appearances, and was also rested for the midweek encounter against Leganes.
Here are the top 10 goalscorers in Europe's top five leagues:
1) Edinson Cavani (PSG) – 29 goals [+2 goals]
2) Lionel Messi (Barca) – 27 goals
3) Robert Lewandowski (Bayern) – 26 goals [+2 goals]