The Argentine superstar is yet to get going at the Ligue 1 club and made it three consecutive appearances without contributing to a goal.
Messi did strike the woodwork with a brilliant, curling free-kick in the first half at the Parc des Princes, but that was his only real highlight.
In the second period of the game, the 34-year-old was fairly anonymous and manager Mauricio Pochettino opted to take him off with the scores level at 1-1.
Messi was unsurprisingly livid at his 76th-minute exit and he appeared to reject a handshake from Pochettino.
The manager's decision to replace arguably the greatest footballer in history with Achraf Hakimi, a right-back by trade, has dominated the narrative in the aftermath of PSG's 2-1 victory over Lyon.
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And that's despite the fact Mauro Icardi scored a dramatic winner in the final minute of stoppage-time.
So it begs the question; why did Pochettino make such a controversial call?
Well, new footage of Messi on the pitch shortly before he was hauled off might go some way to explaining the PSG manager's bold decision.
The video below appears to show the six-time Ballon d'Or winner looking in some discomfort with his knee, with the Argentine manoeuvring it in what looks like a bid to fix an issue.
Take a look for yourself...
Video: Is this why Messi was subbed off for PSG v Lyon?
If you're a manager and see you a player in their mid-30s doing that towards the end of a game, you'd look to sub them off, wouldn't you?
After the match in the French capital last Sunday, Pochettino explained that the decision to substitute Messi was made purely due to concerns over his fitness.
"We made the decision to take Messi off because of a possible future injury," the PSG manager said.
"We have important matches coming up and we have to protect him. These are decisions made for the team and everyone knows we have many great players. We have to make these decisions.
"Sometimes they might be viewed favourably, sometimes a little less."
So maybe, just maybe, Pochettino is being unnecessarily criticised for his decisive call to protect Messi from a potentially serious injury.