The Spanish boat won the 5,264-nautical mile journey from Sanya, China to Auckland by four minutes 25 seconds after more than 20 days sailing.
Abu Dhabi Ocean Racing, skippered by Briton Ian Walker, took the overall lead after four legs of nine with their second runners-up spot in a row.
Dongfeng Race Team (China), victors in the previous leg to their home port of Sanya, were third.
Victory for Fernandez and his crew was all the sweeter after overcoming two major mid-leg setbacks.
Their onboard communications equipment failed at one stage and they could not receive weather data for three days.
Crew member Guillermo Altadill, 22, also suffered a badly injured hand after being swept across the deck by a powerful wave in mid-Pacific.
He will see a doctor on Sunday to discover whether the hand is broken but, for now, victory is dulling the pain.
"I'll see the doctor ... after our party," he told Reuters.
Fernandez took over as skipper for the third and fourth legs to cover for Iker Martínez who is working on preparations for the 2016 Rio Olympics.
The teams will have a short break in Auckland before leaving for the next leg, through the Southern Ocean, to Itajai in south east Brazil.
Overall standings:
1 Abu Dhabi Ocean Racing
2 Dongfeng Race Team (China)
3 Team Brunel (Netherlands)
4 MAPFRE (Spain)
5 Team Alvimedica (U.S./Turkey)
6 Team SCA (Sweden)
7 Team Vestas Wind (Denmark)
(Editing by Sam Holden)
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