The second sentence doesn't make any sense in this context. The first sentence is correct and it means that the call did not connect or that the person on the other end did not pick up (most likely the latter in this case). You might say, "I couldn't get you through" if you were trying to transfer a call and were unsuccessful. The "you" in that case would be an indirect object.

I called you yesterday, but I couldn’t get through. (Good) I called you yesterday, but I couldn’t get THROUGH TO YOU. (This is the correct way to say that, but you wouldn't say "to you" when you already said "I called you".)