If you and your partner took azithromycin for chlamydia does this mean you are clean?

Yes, as long as you weren't sexually active for 7 days after (no oral, anal, or vaginal sex or sharing sex toys -- not even with a condom). You should have been given a single dose of azythromycin (1g) and it should've cleared up quickly. Remember that you both need to get retested two to three months after treatment, every year, and anytime you have a new partner.