The incident happened late in the first half of Tuesday's Champions League match at Celtic Park, shortly after the visitors' third goal in a 5-0 win.
PSG also face a charge after seats were damaged in the away section.
The cases will be dealt with by Uefa's control, ethics and disciplinary body on 19 October.
Police Scotland reported seven arrests at the match, including a 21-year-old man charged with alleged pitch incursion and assault.
He was taken into custody, along with three other men who were accused of assault, breach of the peace and violating the offensive behaviour at football act 2012.
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Celtic manager Brendan Rodgers said he was pleased the rest of the sell-out crowd booed the intruder.
"I think their reaction said it all," he said. "It was disappointing at any ground, at any club, a supporter getting on the pitch like that.
"It was bitterly disappointing and I am sure the club will deal with whoever that supporter was. It shouldn't be anything that we should see.
"I think the stewards dealt with it at the time and I am sure the club will deal with it."
In July, Celtic were fined £20,600 after an "illicit banner" was displayed during their qualifying win over Linfield.
It was the club's 11th punishment in six years relating to misconduct from supporters during European ties.
Following the initial charge, they announced a two-game closure of the area of the stadium occupied by the Green Brigade fans' group.