My girlfriends car transmission recently went out, and my old car that somehow had a tree fall on it, is just sitting in the backyard with a good transmission and engine and everything. So i was wondering would it work to put the transmission from my 2000 chevrolet malibu, into her 2000 chevrolet impala?

This may not be a smart question, but im not much of a mechanic. So any intelligent answers are welcome.

Both cars with the same engine? If they are the same engine then I cannot imagine that they will not work. I would search online for rebuilt transmissions and see if their catalogs show the same part. Also, wrecking yards can use an interchange guide and tell you what will interchange between the cars.