When a gravel base for pavers is installed correctly, weeds cannot grow UP between the individual stones. There is no way that the seeds can germinate and push their way through a compacted gravel. Instead they are most likely blowing or drifting into the cracks on the wind. They will sometimes germinate in the joint sand.
There are 2 main ways to prevent this from happening. One is to keep the paver surface clean . Sweep or blow the pavers off occasionally to prevent the seeds from getting rooted in. You can also use a granular pre-emergent pesticide (like Preen). Gently sweep it into the joints, making sure to not leave any on the surface of the pavers as it may stain them.
The other way is to have polymer sand installed during the installation process. Polymer sand is a granular sand that has an additive in it that acts as a binder to the grains when it's activated. When it's dry, it is hard to the touch and seeds can not root into it.