Ms Ellis delivered Spitfires and bombers during the conflict as a member of the Air Transport Auxiliary (ATA).
She joined the organisation in 1941 after hearing an advertisement on the radio, and flew more than 1,000 aircraft – including more than 400 Spitfires and 47 Wellington Bombers – during the war.
After the end of the conflict in 1945 she moved to the Isle of Wight, where she managed Sandown airport from 1950 to 1970.
Ms Ellis married Don Ellis, a fellow pilot, in 1961. They lived by the runway of the airport until his death in 2009.
She was given the freedom of the Isle of Wight earlier this year, with council leader Dave Stewart describing her as a “national, international and island heroine”.
Reacting to news of her death, head of the RAF Air Chief Marshal Sir Stephen Hillier wrote on Twitter: “Another terrible loss. Mary Ellis, pioneering female aviator, Air Transport Auxiliary veteran, an inspiration to generations.
“I’ll always remember her proudly reminding us at RAF100 events that she was older than the RAF itself! RIP Mary.”
Red Arrows pilot Mike Ling said her death was “more awful news”, adding: “RIP Mary Ellis.
“A legend of the Air Transport Auxiliary. Over 1000 aircraft; 76 different types and over 400 Spitfires alone.
“I hope you’re enjoying a well-earned sherry up there with Joy Lofthouse again. Blue skies Ma’am #LestWeForget.”
RAF veteran Sally McGlone said: “RIP Mary Ellis, you have inspired so many women to fly.
“You will always be remembered, with love and thanks. Blue Skies Thank You. Aetheris Avidi – Eager for the Air.”
Ms Ellis’ death comes after the passing of 96-year-old Geoffrey Wellum, one of the youngest Spitfire pilots to have fought in the Battle of Britain.
There are now three surviving female pilots from the Second World War: Eleanor Wadsworth, who lives in Bury St Edmunds in Suffolk, Nancy Stratford, who lives in the US, and Jaye Edwards, who lives in Canada.