Both sides played out a goalless draw at the Allianz Stadium but it was the fact that Messi was dropped to the bench which hit the headlines.
Barcelona secured their place in the knockout stages of the competition with the hard-earned point, but their Serie A opponents must beat Olympiacos in the final group game to guarantee qualification.
Messi has played 23 games for both club and country already this season.
And Barcelona boss Ernesto Valverde thought it would be best to rest his key man ahead of their crunch La Liga match with second-place Valencia this weekend.
Valverde said: “Leaving Messi out was difficult but he has played a lot this season and today we saw a long and tough contest so we thought a rest would do him good.”
However, Messi’s Argentine team-mate Higuain could not resist having a dig at the 30-year-old.
“The vest fits you well, the vest of a substitute,” Higuain said.
The comment was greeted with laughter by Messi who rarely has to settle for a place on the bench.
He was introduced as a 56th minute substitute in place of ex-Everton striker Gerard Deulofeu.
And he came close to breaking the deadlock but Gianluigi Buffon pushed his effort over the crossbar.