Del Potro beat Russian Karen Khachanov 7-6 (7/4), 6-3 in his quarter-final.
The ex-US Open victor and 2009 Classic champion was broken in each of his three first-set service games and didn't rebound until late in the second.
GETTY IMAGES Roberto Bautista Agut got off to a great start in the final
Having seen the 21-year-old Chung chase down everything Isner fired across the net in the second round, Ferrer was in no mood for long rallies and his plan to look for early winners paid off as he wrapped up the match in 74 minutes.
Bautista Agut earned the championship-deciding break at 5-5 before overcoming del Potro's best efforts to serve out the match and lift the trophy.
"David is a great fighter, we have a great relationship and it's going to be an interesting match to watch".
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"It's incredible to me just to be playing tennis against after all my wrist problems".
In a quality third set, play progressed without any breaks of serve until 5-5 when del Potro slipped behind with his first double fault of the match and then lost two points on his backhand.
Del Potro is seeded 12th in the Australian Open with Bautista Agut 20th, but it was the Spaniard who was in command in Auckland.
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Del Potro, who will move back into the top 10 for the first time since 2014 after a succession of surgeries on both wrists, takes on American prospect Frances Tiafoe and he said the run to the Auckland final had been a massive confidence boost. I've been fighting a lot on the court and I couldn't believe I was playing my best tennis.
"When I saw the ball in, I went insane", Bautista Agut said.
"I started the match very well". Del Potro served better and better as the match progressed and he dropped just 3 points in 5 service games, with another solid hold presumably coming up in game 11.
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They previously formed unified teams in 1991, at the World Table Tennis Championships and the FIFA World Youth Championship both held that year.
"Today the conditions were hard and he was a hard opponent, serving very well and a lefty, playing with a very flat backhand", Bautista Agut said.
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