Tunisia international Ben Khemis, 21, was a free agent after leaving FC Lorient at the end of last season.
Dutchman Kongolo, 19, is the younger brother of the Netherlands international Terence Kongolo.
Both players could make their debut in Saturday's League One opener against Gillingham.
Find all the latest football transfers on our dedicated page.
Doncaster Rovers have signed Issam Ben Khemis on a two-year deal and Manchester City midfielder Rodney Kongolo on a six-month loan.