The Argentinian superstar, renowned for rarely losing his cool despite regularly being the target of brutal tackling, reacted angrily during a confrontation with Roma's French international Mapou Yanga-Mbiwa.
Footage of the first half incident showed Messi aiming a headbutt at Yanga-Mbiwa's after the Roma defender appeared to nod his head in the direction of the diminutive South American star.
A furious Messi grabbed Yanga-Mbiwa by the throat after clashing with the defender before other players rushed over to intervene.
Messi escaped a red card for the incident however, receiving only a caution from referee Javier Estrada Fernandez. Yanga-Mbiwa was also booked.
The flashpoint represented a rare loss of cool for Messi. The Argentine has never been sent off for Barcelona and has only ever been red-carded once -- on his international debut as a teenager in 2005.
Messi's anger soon subsided however as moments after the incident, he doubled Barcelona's lead, making it 2-0 following a superb flowing move involving Luis Suarez, Dani Alves and Neymar, who had scored Barca's first.
Ivan Rakitic made it 3-0 in the second half with a long range strike as Barcelona completed a routine win.
Barcelona kick off the defence of their Spanish league crown against Athletic Bilbao on August 23.
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