The Gorgie side, who entered administration earlier this month, had announced the 21-year-old would join them permanently on a three-year deal starting in July when his six-month loan expired.
However, the deal appeared to be off when administrators BDO came in to sort out the club's financial problems, with striker John Sutton made redundant on Thursday before he signed a two-year deal with Motherwell.
Wilson agreed to take a pay cut to stay at Tynecastle.and the SPFL confirmed the deal would not count as a new registration, and would be allowed under their current embargo.
A statement on the official Hearts website said: "Heart of Midlothian FC is pleased to confirm that Danny Wilson is to remain at Tynecastle following his period on loan from Liverpool.
"The Scotland international's contract with the Anfield outfit expires (on Sunday) but he will keep featuring in maroon after the SPFL confirmed that his registration will continue.
"Although the current administration which the club is subject to has meant an embargo on new player registrations, as the 21-year-old is already registered with the club there is no restriction on his move from Liverpool to Hearts."