Free State Stars mentor Komphela rejected an offer to take up the role last week, preferring to remain in charge of Ea Lla Koto.
SAFA spokesperson Dominic Chimhavi admits the footballing body had their hopes pinned on the former Bafana Bafana captain, who impressed when interviewing for the national coaching job despite losing out to Gordon Igesund.
"No other candidates have been identified at this stage and it is about now going back to the drawing board and the NEC, discussing what options are available," Chimhavi told the Sowetan.
"When the NEC saw the presentation made by Komphela they thought this was a godsend, it was perfect for the role of technical director and exactly what they wanted. They pinned all their hopes on him. At this stage there is no plan B."
SAFA need to replace Serame Letsoaka, whose contract expired in June.