As one of the seeded teams, Pep Guardiola’s side will play away from home at the Red Bull Arena in the first leg, before welcoming the German outfit to the Etihad Stadium for the return game.
The first legs are scheduled for one of the 14/15/21/22 February, with the second legs set take place on 7/8/14/15 March. Kick-offs will be at 20:00 GMT.
The dates of both fixtures are still to be confirmed and ticket and hospitality details will be released in due course.
City reached the knockout stage for a tenth consecutive season having topped Group G, taking 14 points from a possible 18 to finish ahead of Borussia Dortmund, Sevilla and FC Copenhagen.
Leipzig qualified for the last 16 by finishing as runners up in Group F.
Last 16 draw
RB Leipzig v Manchester City
Club Brugge v Benfica
Liverpool v Real Madrid
AC Milan v Tottenham
Eintracht Frankfurt v Napoli
Borussia Dortmund v Chelsea
Inter Milan v FC Porto
Bayern Munich v PSG