Waste is just an unused output. If the output is unusable, or downright dangerous, we probably shouldn't be producing it in the first place (plutonium for example).
Permaculture aims to connect inputs and outputs so that different elements meet each other's needs. For example, if I save my kitchen waste and put it into a compost bin, I can make compost that can then be used to grow crops which I can then eat. I have saved waste (kitchen scraps that produce methane in landfill sites, and need transport to get it there), reduced external inputs (I don't need to buy compost) and increased yields (better soil, more crops, more worms.)
Careful maintenance and investing in good quality long lasting products can also help reduce waste and overall consumption levels.
As they say "refuse, reduce, reuse, repair, recycle". We could add re-design in there too, which is where permaculture makes its biggest contribution.