Similar symptoms, different solution
I recently had a similar problem on my '02, so I thought I'd post my solution for anyone in the future.
Rainy day, left work, went to my truck, found the battery was d-e-a-d. Was able to get a jump from a coworker, and went home on my merry way. Everything seemed fine electrically on the way home, so I didn't think much of it.
Got home, changed, and ran out with the wife and kids to a school function in her car. When we got home, I noticed the 4Runner's headlights were still on.
After a bunch of troubleshooting, it turned out the culprit was some corrosion on the positive battery terminal. Pouring some baking soda and water on the top of the terminal wasn't enough to resolve the problem; needed to remove the positive terminal, wire brush/clean it, and reconnect it. The battery was also 6 years old so I replaced it a few days later for good measure.