Despite it being a pre-season friendly, the pair got into a heated exchange during the first-half at the Nou Camp after Yanga-M’Biwa leant his head in towards Messi and the Barcelona star retaliated by thrusting his own head at the Frenchman before making to grab his throat.
Both could easily have been sent off, but the referee decided to show leniency and only book the pair of them.
Neymar had earlier given Barcelona the lead on his return, while Messi doubled it just before half-time. Ivan Rakitic then added a third midway through the second half to secure a comfortable victory.
Brazil star Neymar and Argentina’s Messi had both returned late to training following their Copa America exertions, but looked in impressive form ahead of Barcelona’s European Super Cup tie with Sevilla next Tuesday, reports Sky News.
The chemistry that saw them, along with Luis Suarez, hit 122 goals in Barca’s treble success last season was evident from the start.
A deep Messi cross was knocked by Jeremy Mathieu into the stride of Neymar, who opened the scoring from close range after 25 minutes.
Neymar then set up Messi, who drove the ball home from the edge of the area after 40 minutes.
The pair were among the players taken off after an hour before Rakitic hit a powerful drive into the top corner from 30 yards to wrap up the scoring after 65 minutes.
“The aim is to keep on the same lines as we were at the end of last season,” said Rakitic after the game.
“I feel strong and the team is working well. This was only a friendly but we still played to win as in any match.”
In the past the Gamper Trophy was the opportunity for Barca to introduce their new players to their fans but due to a FIFA transfer ban Arda Turan and Aleix Vidal were forced to watch the game and will not be available until January.
Pedro, who is a transfer target for Manchester United, did make an appearance as a second-half substitute.
Following the clash with Sevilla, Barca play Athletic Bilbao home and away in the Spanish Super Cup before they meet Bilbao in their first La Liga game on August 23.
