Edinson Cavani gave Uruguay the lead, but Aguero powered home a close-range header from Lionel Messi’s free-kick on 63 minutes to draw his side level.
Luis Suarez put Uruguay back in front five minutes later, only for Messi to equalise two minutes into added time.
Meanwhile, Rodri was an unused substitute for Spain as they defeated Romania 5-0 in Euro Qualification.
The result means Spain finish first in Group F, five points ahead of Sweden.
WATCH: Inside City | Episode 362