The Argentinian dropped every serve in the first set as Bautista Agut, the 2016 Auckland champion, claimed his second title with a 6-1, 6-4, 7-5 victory.
Still, he failed to make an impact with his serve and Bautista Agut broke again in game 4 to open up a 3-1 lead, controlling the points from the baseline and getting some errors from his opponent who still struggled to gain his range.
An wonderful forehand down the line victor moved Bautista Agut a point away from the crown and he sealed the deal when del Potro sent a forehand long, celebrating his second title in Auckland and the 7th in a career.
"It's fantastic to me to be playing tennis again after my wrist problems", Del Potro added.
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Del Potro, who sealed the Auckland title in 2009, shone in the key moments and fought off six of the seven break points Ferrer forged in a tense clash, with two games in the second set lasting nearly 10 minutes apiece.
It was a different del Potro in the second set as he started to find his range and eventually broke Bautista Agut at 5-4 to take the set and level the match.
But the lanky Argentine lived up to his never-say-die attitude and rallied back in the second set, taking advantage of the only break point in the set to force a decider.
Del Potro had said beforehand he expected Bautista Agut would target his inconsistent backhand, but the Spaniard was also prepared to attack the forehand court when the opportunity presented itself.
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He's a great kid; his family are good people, so we're dealing with everything you could imagine to be dealing with right now. They combined for four free throws and Watson hit the final shot of regulation moments later to send it to overtime 65-65.
"I passed really bad moments on the court and in that moment, I scream because I was very stressed", the world No.21 Bautista Agut said.
"Juan Martin is very tough to beat and I think I just played two unbelievable games at the end of the match".
"David is a great fighter, we have a great relationship and it's going to be an interesting match to watch. I tried to have Juan Martin moving around the court". I think I played very aggressive...
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