Try wrapping your Smart Key fob in aluminum foil - in essence creating a small Faraday cage (
http://en.wikipedia.org/wiki/Faraday_cage) that would inhibit any signal between the fob and the car.
Another suggestion I read elsewhere in another forum was that you might be able to store the fob in the glove box and then lock it with the old fashioned key. No idea offhand if that idea would also apply to a Highlander.
Edit: To clarify, the glove box tip above should also mention that the suggestion I found elsewhere implied that the closed glove box would either act as a Faraday cage similar to the aluminum foil suggestion mentioned previously or that it was a "dead zone" incapable of sending/receiving signals between the car and the fob. If you try to store your Smart Key fob in the glove box and are still unable to lock the car, then you may need to resort to foil or one of the bags suggested by TrailDust, at which point you can stash it in your glove box, lock the glove box and the car with your old fashioned key, and go about your merry way.
Hope this helps. Let us know if you get either tip to work.