Goalkeeper Vladimir Stojkovic as well as defenders Branislav Ivanovic and Dusko Tosic were also among those left out after Krstajic's side failed to progress past the group stage at the World Cup in Russia.
Captain Aleksandar Kolarov, Manchester United midfielder Nemanja Matic and winger Dusan Tadic held on to their slots in the 23-man squad published by the Serbian FA on Wednesday.
Midfielder Milivojevic had told Serbian media Krstajic's poor decisions were to blame for defeats by Switzerland and Brazil which knocked Serbia out of the tournament and reiterated his position in an interview with the Daily Mail on Tuesday.
"The game against Brazil, our manager had his opinion, something he wanted to try, and in the end we lost, so that was a bad choice," said Milivojevic, who was an unused substitute in the 2-0 loss to the South American side.
The holding midfielder was substituted in the latter stages of a 2-1 defeat by Switzerland as Krstajic threw on 22-year-old forward Nemanja Radonjic, only to see the Swiss net a stoppage time winner.
"I think we should have been more experienced and played for a result in the last 15 minutes (against Switzerland), we tried to take risks where in my opinion we did not have to," he added.
The Serbians visit Lithuania on Sept. 7 and are at home to Romania three days later in the Nations League's third-tier Group 4, which also includes the Balkan nation's former Yugoslavia neighbours Montenegro.
The first edition of the four-tier Nations League begins next month in the window previously designated for friendly international matches.
It is also linked with qualifying for the European Championship, giving teams a second chance to reach the showpiece event which will be hosted across the continent in 2020.
(Writing by Zoran Milosavljevic; Editing by Christian Radnedge)
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