Video footage appeared to show Ms Black, the MP for Paisley and Renfrewshire South, drinking from a can of lager while travelling from Glasgow Central after a football match between Ayr United and Partick Thistle on Friday night.
The act is prohibited under existing ScotRail policy.
No alcohol can be drunk at any station in Scotland or on board any ScotRail train under a 24-hour ban first introduced in 2020 amid wider Covid prevention measures.
The ban on all ScotRail services remains "under review" after the franchise passed to Scottish Government control on April 1, but no date has been set for it to be lifted.
An SNP spokesperson said: "Mhairi has been reminded of the rules and apologises."
The seven-second video, which was first reported by The Spectator, shows Black taking a sip from what appears to be a can of Tennent's lager.
She is surrounded by fellow passengers on a busy train.
One passenger is shown standing and chanting while holding a bottle of Buckfast in the background behind a seated Ms Black.
Ms Black is a known supporter of Partick Thistle, which had earlier that night lost the clash against Ayr United 3-1 away.
Scottish Conservative MSP Russell Findlay told the Scottish Sun: “The train booze ban has been in place for 18 months - and there’s no exemption for SNP politicians just because their team got beaten.
“Although as a passenger who has to regularly endure the SNP’s nationalised trains, I can’t really blame this MP for wanting a drink.”