Don't worry, this is a perfectly normal reaction for some people when in close physical contact with a lot of men wearing skirts.
Slightly more seriously:
Was it a "sometimes it just does that for no good reason" boner (can I say 'boner' in this forum?) or a "my uke is really cute and not wearing a T-shirt / big and hairy and wearing a skirt" boner?
(I'm assuming you're male, Unregistered)
Being embarrassed is fine, and part of aikido (if you're don't embarrass yourself half the class you're not working at your limit) - the problem comes when achieving wood intimidates and upsets your partner.
So depending on the situation, you could:
1. Ignore it and keep practicing. Working a bit harder, so to speak, should get the blood moving to where it should be. It normally shouldn't show that much when you're moving.
2. Take a water break, if your dojo allows it, while you detumese. You can drink the water, or pour it down your gi if it helps.
3. A couple of breakfalls, a sharp slap to the back of the neck or any strong impact on the body will help lower the salute (the body goes to fight/flight and pulls blood away from such areas - its also good for nosebleeds).
4. Say "Hey, I've just thought of a new way you could throw me!".
5. Wear a hakama. It's a little known fact that most yudansha are aroused all the time. It comes from wearing silky underwear. That's not the knot in their belt - they really are happy to be practicing with you. That's why they smile so much.