The midlife update includes a new insensitive munitions warhead, a more capable fiber optic data link between the launch vessel and the weapon, as well as a change to the fuel system to improve safety.
The deal took longer to negotiate than expected and the entry into service is later than originally planned, said a spokesman for the MoD.
"BAE Systems' original proposal could not be accepted by the MoD. As such, both the MoD and the company have been engaged for some time to develop the upgrade project and resolve commercial issues. A further proposal from BAE Systems has been accepted by the MoD and a contract awarded.
"The delay will result in the new upgraded Spearfish torpedo entering service later than originally forecast. However, it is only right that the MoD must obtain the best value for money for the taxpayer and defense," said the spokesman.
"We have worked hard with the MOD to reach an agreement on the Spearfish Upgrade Programme; we are delighted with the announcement by the Secretary of State today and regret that we are unable to provide any further detail on contractual negotiations," a BAE spokesperson said.
BAE said in a statement that initial deliveries of upgraded torpedoes are set for 2020 with the final revised weapons being handed over in 2024.
The company began the assessment phase on the Spearfish upgrade in April 2010 in a deal worth £40 million.
Spearfish has been in full production for the Royal Navy since 1988 and the final weapons came off the BAE production line in 2003.
The weapon, which can be used against underwater and surface targets, is fitted to all current Royal Navy submarines including the new Astute class hunter killer and the Vanguard ballistic missile boats.
A spokesman for the MoD said that on current plans the weapon would also be fitted to the upcoming Successor class of Trident armed nuclear missile boats slated to start entering service at the tail end of the next decade.
The current torpedo capability contract between the MoD and BAE expires mid-2019 and a follow-on support contract is expected to negotiated by the two sides.
With an upcoming election due for next May defence secretary Michael Fallon emphasised the handful of new jobs the deal had created in the Portsmouth area, where BAE's Maritime Services business is based.
"This contract award is good news for the Royal Navy, the UK and the city of Portsmouth where around 100 engineering jobs will be created or sustained," he said in a statement.
Portsmouth has been hit this year with the closure of BAE's naval shipbuilding facilities in the town.
The company retains warship support capabilities in Portsmouth and secured a £600 million contract earlier this year to run the naval base, which is scheduled to be the home of the two Queen Elizabeth class aircraft carriers now being built by an industry alliance led by BAE.