Mrs Ellis was a member of the Air Transport Auxiliary (ATA) and delivered Spitfires and bombers to the front line during the conflict.
She said she had flown "about 1,000 aeroplanes" during the war, before moving to the Isle of Wight in 1950 to take charge of Sandown Airport.
ATA secretary John Webster described Mrs Ellis as an "amazing" person.
While she was commonly known as the last-surviving female pilot from the war, in fact there are three others.
Mr Webster said that one, Eleanor Wadsworth, lives in Bury St Edmunds, another, Nancy Stratford, lives in the US and the other, Jaye Edwards, lives in Canada.
Mary Ellis, then Mary Wilkins, joined the ATA in 1941 after hearing an advertisement for women pilots on BBC radio.
She said at the time they were known as the "Glamour Girls", adding: "There were plenty of escorts around."
She married Don Ellis, a fellow pilot, in 1961, and continued to live in their marital home beside the runway at Sandown after his death in 2009.
Speaking at a surprise party in 2017 for her 100th birthday - held at the airport - Mrs Ellis said the Spitfire had always been her favourite aircraft.
"I love it, it's everybody's favourite," she said. "I think it's a symbol of freedom."
Tributes have been paid to Mrs Ellis by fellow pilots, including Red Arrow flier Mike Ling.
He posted on Twitter that she was a "legend of the Air Transport Auxiliary".
"I hope you are enjoying a well-earned sherry up there with Joy Lofthouse [a fellow ATA pilot] again."
RAF veteran and military historian Sally McGlone also paid tribute to her.
She wrote on Twitter: "Older than the RAF by one year.
"Without the ATA #RAF100 might not have happened."
Author and former RAF navigator John Nichol described Mrs Ellis as a "truly remarkable lady".
He added: "Another giant leaves us to join her heroic friends in the blue skies."