He died of natural causes.
For reference and for anyone who doesn't know about the supreme court justices. The current US supreme court justices are:
Chief Justice John Roberts Antonin Scalia( deceased) Ruth Bader Ginsburg Sonya Sotomayer Stephen Breyer Samuel Alito Clarence Thomas Anthony Kennedy Elena Kagan
This means that there's potentially two positions that are up in 2016 once the new president gets elected unless Obama chooses Scalia's successor before his term ends.
I'm saying two because, I know in the past it's been said that Kennedy might retire and obviously Scalia's position is up for grabs.
Also, in general usually Thomas and Scalia have notoriously been the most conservative and by the book constitutionalists of the nine supreme court judges.