Be honest. You made a mistake, acted in a way you're now embarrassed of, and want to patch things up. You'd be surprised how far a bit of humility will go in these situations. If you've been acquaintances for 3 years this other guy likely knows you well enough to see that you're genuinely apologetic for behaving the way you did.
Even if things don't get immediately back to normal, if your acquaintance is an even tempered person and all you did was at worst yell at him he will likely want to patch things up as well.
I would first contact him in a nonconfrontational way: email, text message, or some other method where he doesn't have to immediately respond or worry that you're going to scold him again. Say something like, "I want to apologize; can we talk?" Offer circumstances as if you were setting a date or a meeting: "We can get coffee on Thursday or Friday" or even "I can meet you outside the dining hall after Biology."
When you meet: admit fault, say how you feel, clearly apologize, and request forgiveness. An example might be, "I misunderstood something and scolded you. Now I feel embarrassed. I'm sorry for doing that. Can we put it behind us?"
It'll be a difficult conversation to have. He might not accept your apology or be willing to forgive you. If he doesn't, that's fine. You can't force him to overlook your mistake.
It's never too late to set the record straight when you were wrong. Your present feelings indicate that the issue is truly not resolved. Own your feelings and look for a way to make it right. By that I mean that it may not be clear with your friend that you know you were wrong.
Find a time/place where you are alone. Bring it up. Say you were wrong for two reasons: That you were wrong in the first place, and that you waited so long. Then apologize for both. One would hope that it would lead to better feelings for both of you.
Just be straightforward, and honest. You could do it by email if you don't want to do it in person. A simple message stating how you feel about the incident, followed by an apology will do. I'm sure the other person will respond with their thoughts about what happened, and how they feel about it. Whether that person will accept your apology, or not, is upto them. But you tried, and that counts. Good luck!