Hanna is basically correct, but I would add that "over the phone" generally tends to emphasize that the conversation was NOT "in person / face-to-face," or by email, or by snail mail, or by two-way radio, or by Skype, or by telepathy, etc. -- it was по телефону. So "over the phone" is often used in answer to a question about the method of communication:

"I finally reached an agreement with Mr. Jones about the business contract yesterday."
"Oh, did you have a lunch meeting with him?" (i.e., "did you speak in-person" or "did you talk face-to-face")
"No, I invited him to lunch, but he's traveling out of town -- so we spoke over the phone."

It would be rather unusual to say "I'm talking over the phone right now" as a present-tense construction -- I mean, how often is it necessary to emphasize, "I'm using the telephone as a method of communication right now?" But if you say "I'm talking on the phone now," the meaning is more like "Be quiet, don't bother me, I'm speaking to someone else."

Of course, "I'm talking over the phone right now" could be an answer to a question such "Are you chatting with your friend in Australia by IM?" -- "No, I'm talking to him over the phone right now, long distance -- and paying by the minute!!" Again, "over" is used here because "the phone" is being compared/contrasted with a different form of communication, in this case Instant Messaging.