The Premier League leaders have fallen victim to storms Dudley and Eunice as winds reach up to 100mph.
The back-to-back storms have caused amber weather warnings across the UK with power cuts and travel disruption expected for much of the country.
A club statement read: "We can confirm the plane transporting the first team home from Lisbon has landed safely in Liverpool, after high winds forced a diversion from Manchester."
Man City were on their way back from Lisbon after a 5-0 destruction of Champions League last 16 opponents Sporting CP, as good as booking their place in the quarter-finals.
A Bernardo Silva brace alongside efforts by Riyad Mahrez, Phil Foden and Raheem Sterling put the Portuguese champions to the sword at the Jose Alvalade in the Portuguese capital.