Appointed between Nov 17, 2003 and Aug 31, 2004, the staff, however, will be able to apply if any circular on new appointment is issued, the two-judge bench said in the verdict.
The termination will come into effect immediately after pronouncement of the verdict Monday, the court ruled.
The NU has been asked to complete the process of fresh recruitment to the posts in six months.
The HC bench of Justice Hasan Fayez Siddique and Md Jahangir Hossain passed the verdict on completion of hearing of a writ and a review petition.
The 1,100 employees can apply for fresh appointment. If they do, the provision of age limit will be considered in their cases, the HC said.
But they will have to sit for written and viva voce tests, the court added.
The court directed the NU authorities to publish advertisement for recruitment at least five national dailies.
The 1,100 were appointed to different posts of the university including deputy registrar, assist registrar, section officer, programme officer and driver.
Police unearthed the irregularities in an enquiry.
Advocate Jafar Ahmed said the enquiry found anomalies in advertisements and recruitment process.
Lawyers Rafiq Ul Huq and Rokanuddin Mahmud argued the case for the NU employees while deputy attornmey general Biswajit Roy represented the state at the hearing.
Awami League MP Fazle Rabbi Mia, also a lawyer, challenged the legality of the appointments in 2004. A High Court bench in 2006 dismissed his plea.
Gazipur MP A K M Mozameel Haque on Dec 15, 2010 filed a review petition and the High Court on Aug 23 last year ordered the university to sack the staff.
The Appellate Division on Dec 4 last year overturned the High Court’s two earlier verdicts and ordered a fresh hearing after the fired employees filed three appeals.
Monday’s verdict was issued following the Appellate Division order.