Yes. The most important thing is to build an embassy with the rival civs. To do this, you must first have the Writing Tech. From the game map, look at your capital city. A star icon will be right next to the capital name. Click on this to start creating embassies. It does cost gold, so make sure you have your treasury high enough to afford it.
As long as you have a road and/or sea (with harbors) network connected to the AI capitals, you can begin trading resources, making Right of Passage agreements, and Military Alliances.
Once you obtain the Nationalism Tech, you can then begin forming Mutual Protection Pacts.
As has been mentioned, to form these agreements just make contact with the civ in question. At the top of your (or their) trade screen you will see the options for alliances and what-not.
Now, you asked how to make them stop. Well, once they gang up on you and declare war, you are in for some serious warfare. They will refuse your envoy (any kind of communications), basically, until you kick their tails in enough that in is in their best interest to make peace.
Try to single out the head honcho, the civ that began the warring in the first place (in your case Japan). Maybe if you pound on them, Russia and France will be more willing to make peace.