Two fine solo tries from Roma Fraser at the end of each half kept Glasgow in touch of Thunder but the hosts scored in the dying minutes to seal the win and deny Warriors a bonus-point.
The Celtic Challenge now splits for the play-offs, with the top three teams facing each other for first to third positions and the bottom three for fourth to sixth.
Thunder and Glasgow both finished in the bottom half along with the other Welsh side Gwalia Lightning, while undefeated Wolfhounds will play Edinburgh and Clovers for the title.