I have the same problem. Shoes are DMT Ultimax RSX and pedals are Campagnolo Pro-Fit. I use a small, gel insert right at the pedal axle, about the size of a fist. A large, sporting goods store should have them. The pain does not go away completely, but it's much, much better than before. Before I tried the gel insert, I would constantly move my feet inside the shoe to keep the pain at a reasonable level. Needless to say, it made for a less enjoyable ride.
I think a thicker gel insert will stop the pain, and I'm looking for a thicker insert I can carve up.
As martin_i001 suggested, I do agree that a different pedal with a wider platform might help. I already have 6 sets of Pro-Fit pedals, so the investment to change them all would be quite expensive. I'm hoping the gel insert will work.
Lastly, carbon sole shoes are nice, but they have a tendancey put your feet to sleep. They are not for everyone.
-Wm.