Unintentional Plagiarism in my Masters Thesis
While I don't know the policies of your university, nor anything about your advisor, I would suggest that you explore any possible option of submitting a corrected version of the thesis. Explain to your advisor what happened. Be very clear and honest about it. Perhaps they can make an accommodation. The paper, on which it is based can, perhaps, be used to show proper intent. 

If you can't substitute a newer version, you will need to create and try to submit an addendum giving proper credit wherever needed. 

I doubt that the paper is in any danger of being rejected, since the citations are correct there. 

While many might consider this a serious breach, rather than panic and carelessness, I doubt that it would be career ending. Intent matters a lot in such things.