Holidaymakers were flying back from the south of France to Heathrow on a Boeing 757 when the toddler was allowed onto the flight deck.
She then perched on one of the pilot's knees and was allowed to press buttons on the instrument panel.
A BA spokeswoman confirmed that, following a passenger's complaint, the captain, Phil Higton, and his co-pilot were under suspension.
She said: "We have suspended them pending an investigation. We do view it as a serious breach of company regulations but it is important to stress that at no time was the safety of the passengers compromised.
A newspaper named the girl the girl as Emily Pickersgill and said she spent 20 minutes on the flight deck, at one stage pressing a button to make the plane turn.
It also said the plane was 15 minutes from Heathrow, although the BA spokeswoman said this was unlikely.Reuse content