So plan to replace my front and rear sprocket and chain on my xv125, it uses a stock 13 tooth front and 47 tooth rear, 

If I replace the rear with a 45 tooth, what what effect will this have on the bike?

 

 

you will have higher revs and more fuel consumption for the same speed but it will excelerate a bit quicker with a lower top end speed :-)

Nope Keith, the result will be the opposite of what you've described :-) -  replacing a 47 on the back with a 45 will mean verrrry slightly lower revs at any given road speed and verrrry slightly better fuel economy. 

I doubt either would be noticeable and with such a small change in overall ratio, I doubt anyone would be able to detect any change in acceleration.

The only noticeable effect might be the position of the wheel spindle in the swinging arm and how that could affect chain tension adjustment - it will sit further back and will reach the end of the adjusters earlier, if you keep the chain on long enough to let it extend/wear that much.

IMO, if you go ahead, you'll not damage anything and you'll hardly notice the effect (a dirty air filter will have more impact on acceleration).

Yes if you do check the chain isnt rubbing more against swingarm if it does that already.