Replacing one bass speaker for 2001 Toyota Avalon

can you replace only the bass speaker on JBL system?

Yes it can.

If you can’t find OEM, make sure what you replace it with will fit where the old one was. Make sure it has the same impedance (look for the Ω symbol) and it should be fairly close to the wattage rating as well, and never under - if the wattage rating is too low your amp might blow it, and if it’s too high your amp might not be able to drive it very well.

Places like Crutchfield can help you select a good replacement speaker.