I think you did the right thing by calling. It's just too unlikely that happens what has happend.
The chance he has a flush draw is about 8% (1/3*1/4). The chance the flush hits is a little over 20% (9/43). For a chance that you are beat about 2% of the time its just not worth giving up 20% of your stack. Just in case you are absolutly sure that he has the flush-draw (in addition to the ace) folding would be right.

Greetings
Dancer