At the end of Season 2, how did the trio Peter+Walter+the Olivia from the other universe manage to come back to our universe? I had understood than only Olivia from our universe had the special ability to jump from one universe to the other ...

you're forgetting Belly and Walter's discussion earlier on in the lab. everybody is essentially an atomic bomb's worth of potential energy. if the atoms of our body (in this case Belly's) are activated, then we theoretically can expend the above mentioned amount of energy. so Belly essentially blew himself up with the aid of that device and this energy was sufficient to send the trio home. hope that helps.