Which version is correct?
As discussed with you over the phone.
As discussed with you on the phone.
Either works just fine as written. Pace @JasonChen, “on the phone” works quite as well as “over the phone” as an adverbial phrase for modifying a verb of telling, and actually appears to have been more common since about 1957.
It depends on the context of the sentence.
You can say that you "told someone over the phone." This means that you told them using your phone. "Over the phone" is usually applied when you tell someone something.
You can also say that you are "on the phone." This means you are calling someone.
In this case, "over the phone" is correct, since you are telling the person something.