I want to lodge a Prospective Marriage visa, but my partner is still waiting for his divorce. Can I lodge the visa application?

You cannot lodge a Prospective Marriage Visa unless you are both free to marry. As your partner is still married, he is not free to marry you. You must therefore wait to Lodge the visa, or consider a regular Partner Visa, as you can still consider yourselves to be a de facto couple, even though he has not  yet divorced.