Informing supervisor for declining Research fellowship position in light of PhD offer
Could the PhD position wait for a later starting date? Would the internship be open to a shorter period? Could flexibility on both sides be good enough to bridge the gap? I imagine that writing polite emails to both involved parties might go a long way to fixing your problem. 

It may be that funding restrictions do not allow the PhD offering university to delay by too much. But it may also be that the starting date is flexible on their end. There is no way of knowing before you ask. Ensure that your message clearly indicates that you are overjoyed to accept their offer, but that you do want to do right by this other university that invested resources in you.

Simultaneously, the other university should see that a fully funded 4-year PhD is a better job offer than a one-year internship. So your email to them should express thankfulness for the effort they put into the visa application, but should also indicate that for career purposes you cannot really afford to decline a fully funded 4-year position.

Sketch a scenario where everybody wins. Maybe you can convince the research internship that you can do a great job in their department from January 1 until August 31, and maybe you can convince the other university that a starting date of September 1 is better for all involved. There may be operational constraints that disallow this, but you won't know until you ask.