The hosts were well on top in the first half and should have gone in further ahead than just the opener by Tijjani Reijnders.
Phil Foden fired wide, Bernardo Silva saw an effort just clear the crossbar while Erling Haaland had a shot well saved by Filip Jorgensen before blasting against the post.
Chelsea came out after the break with fresh endeavour and had their own opportunities through Pedro Neto and Liam Delap but the hosts looked well on course for all three points.
But the visitors found a last-gasp leveller deep into stoppage time through Enzo Fernandez who poked home at the third time of asking.
View our extended highlights package above.
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