I have also been looking for the solution to this problem, except I want to EQ "down" the bass line in order to play over the track. I have found that Transcribe! is the closest tool to meet my needs.
Here's what I do:
1) Use Transcribe! to learn the bass part.
2) Use Transcribe to EQ down the bass part. You can't eliminate the bass line completely, because the bass and kick drums also live down there along with the bass. If you use the provided filter the whole song becomes "dead". So I use a custom EQ curve to diminish the bass; I'll be playing over it anyway.
3) Export the file as a wav; make sure you include the EQ settings.
4) Import the wav file in Audacity.
5) Set Audacity audio to play back through speakers and record through microphone.
6) Mic your bass amp. (I use a USB mic; it's all I have).
7) Connect a pair of headphones to the computer's headphone jack (this way you can listen to the track but you don't get any feedback on your recording).
8) Hit the record button on Audacity. You'll end up with two tracks: your previously imported wav file and your recorded bass line.
I have found that it is a nice learning tool (recording yourself that is). Unless you use an audio interface, lag is going to be somewhat of a problem.
For a sample of this setup, visit
my blog. The bass lines you hear there is me playing over the track. The original bass line is barely noticeable. I've been playing for one year, learning on my own as time and family/financial priorities prevent me from getting an instructor.
I am learning keys so that I can come up with my own versions of the songs I like. I'm thinking of a pad controller for the drum part.
It's not the best setup but it's what I do and I'm learning and having fun at the same time.