The DNA evidence is ambiguous, since Thomas Jefferson was not the only Jefferson male in the vicinity.
The main argument in favor is the oral tradition among Sally's descendants, that Sally had children by Thomas Jefferson.
Madison Hemings, one of her children, told the census taker in 1870 that he was the son of Thomas Jefferson; the census taker was sufficiently impressed that he made a note of that on the census form (clearly legible on the microfilm of the census record). Later, in 1873, a newspaper in Pike County, Ohio, carried an article about Madison Hemings being the son of Thomas Jefferson, evidently based on what Madison had told the author.
There is a good short treatment of this in Willard Sterne Randall's Thomas Jefferson: A Life (1993). The late Fawn Brodie, who did more than anyone else to revive interest in the Sally Hemings story, located several of her descendants who claimed to have heard of their descent from Thomas Jefferson from family tradition.
Sally's mother was a mulatto, so she was no more than one-quarter African by ancestry.