I did that to mine when I smacked my roof-top box into it. I pushed it back down but it would not stay. You could try pushing it back down and tightening the nut that holds it. I solved the problem by replacing it with a low-profile version. This thread will explain:
http://www.toyota-4runner.org/5th-gen-t4rs/215885-low-profile-xm-shark-fin-antenna-swap.html
One has to pull down the headliner at the rear. Remove the snap buttons, carefully pull it down a bit, and reach in there and tighten the nut. It is a tight fit, take your time and you will not crease the headliner. As stated above, this did not work for me, the roof metal was bent a bit right at the spot where the nut goes through the roof. You may have done the same thing. I flattened it when I installed the low profile antenna. You may have to remove the antenna nut, lift the antenna, and bend the roof flat as I did.How do you access the "nut" to tighten? Is it under the plastic fin cover?
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