The 40-year-old gangster was shot multiple times in the car park of his apartment building in Rhodes on June 27 and later died in hospital.
Detectives from the State Crime Command's Homicide Squad established Strike Force Claypinch to investigate, which subsequently formed part of inquiries by Taskforce Erebus into several fatal shootings and criminal activities by Sydney crime gangs.
Strike force detectives raided a property at Blair Athol in Sydney's southwest around dawn on Wednesday, arresting a 25-year-old man who was taken to Campbelltown Police Station and charged with murder.
Two more search warrants were executed at homes in Mt Pritchard and Kemps Creek with detectives seizing cannabis, cash, electronic devices, and other items relevant to the investigation.
The accused man was refused bail to appear at Campbelltown Local Court later on Wednesday.
Police will allege in court he was involved in the planning and co-ordination of Nazlioglu's murder.
In 2020 a jury found Nazlioglu not guilty of murdering Comanchero boss Mick Hawi, who was gunned down at Fitness First in Rockdale in 2018.
Nazlioglu was accused of being the balaclava-clad gunman, while Jamal Eljaidi was said to be his getaway driver but was also acquitted.
The Crown alleged Nazlioglu was motivated to kill Hawi after the former close friends fell out with the relationship souring during a fishing trip to the Central Coast in the summer of 2016/17.