I went through the same thing with my son. Tiny red bumps on his cheeks, nose, chin area. I had suspected it to be a "food allergy" at first. But his doctor said if it was a food allergy, his body should be covered in rashes -which he didn't have the red bumps anywhere else except for his face.
So after much thinking back on what we had done differently, I realized that dh and I was washing our own clothes with fabric softener. We were also using it on our bedsheets. I thought maybe because he would rubb his face on our shoulders and on the bed sheets, it could be an allergic reaction to that. So got dh to re-wash all our clothes, including the bedsheets, and strangely his red bumps started to heal and just went away.
So my guess is that it is an allergic reaction to something that your son has also. His doctor had prescribed him a 1% horticortisone cream, but that's because he had thought he had eczema...but it wasn't.
What I did was, wash his face with a very mild soap, i used dove baby. I washed it maybe twice a day. Then when he goes down to bed for the night, i applied vasaline on his face just to keep the moisture in. It seemed to help.
Give it a few weeks and it will go away. It's just a temporary thing. But i know how you feel!!