The theft took place over several years from a huge industrial site in the city-state, described by the Anglo-Dutch firm as one of its most important production centers in the world, authorities said Friday.
Police put an end to the scheme, which saw oil siphoned from the refinery and sold below market rates, in 2018 with the arrest of several suspects and the seizure of a tanker and money.
Captain of the tanker, Doan Xuan Than, was jailed for five and half years on Thursday after admitting he received stolen oil worth $5.7 million, the attorney-general's office confirmed.
The 47-year-old worked with three other men, who remain at large, in a scheme to buy the pilfered crude over almost two years, according to court documents.
The oil was allegedly illicitly purchased from Shell employees and later offloaded at sites outside Singapore.
For his role, Than earned between $70,000 and $90,000.
He was the second person jailed over the massive theft after a Vietnamese crew member from his tanker was handed a two and a half year term in July, according to Singapore media.
The cases of 11 former Shell employees are still pending, the Straits Times newspaper reported.
Singapore is one of the world's largest oil trading hubs with huge quantities of crude from the Middle East passing through the city-state before going on to East Asia, and several oil majors have local refineries.