The Scottish Premiership side announced on Thursday that the 28-year-old has been suspended as a precautionary measure following his report of an alleged incident to his superiors.
In a statement, St Mirren vowed to "undertake a full investigation" and would make "no further comment during this process".
On Friday, Police Scotland confirmed Rooney had been arrested and charged and is due to appear at the city's sheriff court at a later date.
A spokesperson for the force said: "A 28-year-old man was arrested and charged in connection with an assault on an 18-year-old woman and a breach of the peace against an 18-year-old man in takeaway premises on Queen Street, Glasgow, in the early hours of Thursday September 19, 2024.
"He was released on an undertaking to appear at Glasgow Sheriff Court at a later date.
"A report will be submitted to the Procurator Fiscal."
Rooney returned to Scottish football in the summer following a spell with Fleetwood Town, having previously played for various teams including St Johnstone, Inverness Caledonian Thistle, Queen of the South, Dunfermline and Queen's Park.
Speaking at his pre-match media conference on Friday, St Mirren manager Stephen Robinson said: "The club and board have taken a decision to further investigate the incident. That's as much as I can tell you, really.
"He spoke to the club and made us aware of an incident and the club are investigating.
"I'm not really involved in that decision. It's a board level decision and I've got to concentrate on the football side of things."