First off, welcome to Psych Central.

I should point out that an ex of mine is a very similar way. She stole my phone when I wasn't looking and put her number in it; that's how I "got her digits"; it was inappropriate, like so many things she says/does, said/did. But anyway, yeah, I recommend getting some help to understand why you do these things and to see if you can break the habits you might have. Anywho, point is, I'm still pissed off, 6 years later; it was wrong, and although I may have seen it as sweet or something at the time, she shouldn't have done it, ... but I like to think I can be understanding and... bend my usual way of thinking, now and again... she probably didn't know how to go about it. What pissed me right off, was, a while after being together, she started getting paranoid about me and someone else, so once again nicked my phone and went through it while I was in the shower! The cheek!

You could just be blunt; be straight-out honest with him. If you are as joint at the hip as you say, he may just understand. Something like,

"I have a confession to make. I'm really sorry for this. I did something I'm not proud of, but I didn't know how to tell you that I have feelings for you that go far beyond friendship. When you gave me your phone, I saw that you were on [the site's name] and couldn't resist but to have a look. I'll understand if you're angry, but please understand I only did it because I genuinely like you and didn't know how to go about showing that."

Honestly, I think that's what I would personally say, ... depending on the situation and my stance with them.

PS
Come to think of it, what my ex did was far worse. lol His account is public, anyway, and he did hand the phone to you, knowing full-well that you could've inadvertently seen all sorts... he may have even done it intentionally. 'o.O Some guys do weird things, just like women. Think of this way, ... him being on that site tells you that he wants something, be it a relationship or fling, and so, perhaps you know he's available, or at least at the early stages with someone else.