United said earlier this week they were no longer planning a bid for the 18-year-old due to work permit issues. Reports say Ljajic would have cost the English side 10 million pounds.
"Manchester United's decision will inevitably force us to change our business plans, meaning that we will have to sell more players than we would like to in January," Partizan's director Ivan Tomic told Belgrade media on Saturday.
"This is a heavy financial blow to us and it certainly hasn't made anyone at the club happy.
"As far as Ljajic is concerned, he is obviously disappointed but I am sure he will bounce back very quickly and prove his worth, he has a great future."
General Secretary Darko Grubor added: "It is a shame the deal fell through but life goes on and we will survive without the money we would have got from selling Ljajic."
Partizan are chasing their third consecutive league title and are one point behind leaders Red Star Belgrade with two games left before the December-February break.
They are at home to fourth-placed OFK Belgrade on Sunday behind closed doors after they were punished along with Red Star for crowd violence during their derby last Saturday.
