Former Socceroos forward Williams confirmed his departure on Tuesday, ending a one-season stint in Wellington which reaped 11 goals.
The 31-year-old formed a potent combination with Johnny Warren Medal winner Krishna, who announced the end of his five seasons at the Phoenix last month.
Neither player has revealed their next destination. Both have been reported to have offers from Asia.
New Phoenix coach Ufuk Talay faces a hefty rebuilding job, with all five visa slots to be filled and negotiations continuing with veteran skipper Andrew Durante.