You can explain it in an age appropriate way. My son is 3 and his "real" dad doesn't want anything to do with him either, hasn't seen him in coming up for a year now, never sends birthday cards, texts to see how he is, anything.
When he started calling DP "My Daddy" I just had a little chat with him, and said, yes DP is your daddy and you can call him that if you like, but did you know you have another daddy?
He was very intrigued but didn't really understand, he kept asking who, who is my other daddy? I told him his name and then someone said maybe you could show him a picture? So I went through the computer and found the pictures from when he was a baby/before he was born which luckily I hadn't deleted, and he was able to look at them. Every now and again he asks to look at the pictures, but he never asks to see his dad or why he isn't around. If he did ask, then I would just say I don't know, I think he must be busy with work. When he's older, he will probably figure out for himself that his dad didn't want to know, but he will be older then and better able to deal with it, especially if he's known all along that there's another Dad in the background.
You don't have to explain at this stage about sex and genes and which one is his biological father, because when he's old enough he'll work that one out by himself, but it is best to tell him that he exists so that it doesn't come as a huge shock later.
DS isn't really emotionally bothered about having another dad, he just takes it in his stride. As far as he's concerned, DP is his dad and that's fine by me. When we look at pictures he once asked if we could print one out, so I let him choose one, and the one he chose didn't even have his dad in it!
DS has a half brother, but I haven't told him about him and I probably won't unless he asks. He did meet him but doesn't remember him at all.
Your son won't be the only one in his situation - it's sadly fairly common for dads to just disappear :( if he knows the truth it will be easier for him to understand etc later. Does he have any friends who have stepdads? Maybe you could explain it to him using them as an example.