Two other absconding accused have been jailed for two years in the case started in April, 2010 for conducting a campaign against the state and storing Molotov cocktails or petrol bombs.
Judge Mujibur Rahman of an anti-terrorism tribunal finally delivered the verdict having deferred it seven times.
Besides the two-year jail term, Touhidul Alam and Saidur Rahman were fined Tk 5,000 each.
They will have to spend three more months if they do not pay up.
Mohiuddin, a professor at the Institute of Business Administration, was present at the tribunal.
The judge ordered police to arrest the two absconding convicts, the tribunal’s clerk Ataur Rahman told bdnews24.com.
Mohiuddin has been acquitted despite being the chief coordinator of the banned Islamist group perhaps because one of the two investigators did not testify in court, state counsel Jahangir Alam Chowdhury told bdnews24.com.
The state will decide about filing an appeal against the verdict after getting the full version, he added.
Police arrested Hizb ut-Tahrir members Tanvir, Saidur, and Touhidul when they were distributing leaflets and sticking posters with false information outside the Taqwa Mosque at Uttara in the capital on Apr 18, 2010.
Bombs were also found in their possession, according to the charges.
Police accused Mohiuddin of ordering the operators of the organisation to carry out the activities against the state.
Police added two more accused to the case later and charged the six in 2013, but the court forwarded the matter to the home ministry as cases under the Anti-Terrorism Act need the government's clearance.
The court took cognisance of the charges after the ministry cleared the case in 2016.
The government banned Hizb ut-Tahrir on Oct 22, 2009 for running extremist activities against the state.
Over 50 cases have sincevbeen filed against party leaders and activists.