Whether the ?24million summer signing from Inter Milan will come into contention for the home FA Cup quarter-final with npower Championship side Reading on Sunday remains to be seen.
Balotelli, 20, eventually came off in the 57th minute after being over a minute late coming out for the second half with City losing 2-0 in the last-16 first leg game. He appeared in some distress and was constantly rubbing his face before being replaced by Carlos Tevez.
Mancini said: "Mario had an allergy, I don't know what, his face was swollen, I don't know why. He wanted to play in the second half but he had this problem 10 seconds before coming out.
"I came out a minute before the players and I didn't see Mario. He then said he could play but his face was swollen."
It is understood Balotelli is allergic to certain types of grass.