A team spokesman said the former Force India deputy principal, who was appointed president of McLaren Indycar last November, would have been out of contract after the race but had departed on Sunday.
Fernley, who had previous involvement in North American racing, had warned back in November that McLaren faced a major challenge. The extent of the failure came as a major shock, however.
McLaren are three-times Indy 500 winners -- in 1972 providing a car for Mark Donohue as a private entry and in 1974 and 1976 as a works entry with Johnny Rutherford -- but their return was beset with problems.
Alonso, who led the race in 2017 in an Andretti Autosport entry before an engine failure, crashed his Chevrolet in practice on Wednesday and the Spaniard then missed nearly two full days of practice while a back-up car was prepared.
He tried five times on Saturday to qualify, puncturing a tyre on the first attempt, and failed to get the speed needed in Sunday's shootout.
"We came here to race and to challenge ourselves and we were not quick enough. I congratulate all the other guys that did a better job, and hopefully, we'll see a nice show next Sunday, with everyone safe," said Alonso.
"I will be enjoying from the TV, unfortunately."
Alonso wants to complete the so-called Triple Crown, a feat only previously achieved by the late Briton Graham Hill, by adding Indy to his Le Mans 24 Hours and Monaco Grand Prix successes.
"You're a champ, let's go and win the Triple Crown," McLaren's American boss Zak Brown had told him over the team radio as the Spaniard ended his Formula One career in Abu Dhabi last November.
Former Indy 500 winner Gil De Ferran, McLaren's Sporting Director, on Sunday apologised to Alonso, fans and sponsors for the failure.
"In my 35 years of racing, this is the most painful experience I've ever had, but we are racers," said the Brazilian.
"We respect this place and it is one of the toughest challenges in racing. This experience will only make us stronger as a team, and we want to come back."
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
Share
