Um . . .
Talk to your players? Tell them you have an idea but it involves their characters being captured. Ask how they want their characters to be captured. If they want to fight it out, use non lethal attacks, sleep and paralysis poisons and will save spells as someone suggested. If they don't, have at least two or three times their number in guards show up to capture them and lead them off. Heck, maybe the players will help you plan how to capture their PCs! Get ideas from them and they will probably be more willing to go along with it!
I think the reason that players are very leary of this is because of the importance of items. Take away a 4th level, or higher, character's equipment, and a big part of the character is now gone. Tell your players you aren't going to ruin or destroy any of their equipment and work toward them recovering their items by the end of the session they are captured. If it can't be done that session, tell them you are working toward that goal and they won't lose anything.
After they see that they can trust you not to mess with their characters, they will be more open to these types of situations. It might be that you can tell them they know they are going to be overwhelmed if they fight but they know if they surrender they will be treated well. (This would be something else to set up: Rules for fighting and surrendering in your game and how it is handled by the various peoples.)
Having said all of that, I would highly suggest not using a known evil villain or monster when doing this. Being captured by drow or beholders is probably never a good thing. However, being captured by city guards or even the thieves guild while not the best situation isn't the worst either.
Communication is the key! Let the players know it is for the story and it will make sense! That will make them more likely to go along with the idea.
A few coppers for you. I hope they help!
Have a good one! Take care!
edg