Second-seeded del Potro, champion in 2009, beat four-time champion and eight-time semifinalist David Ferrer 6-4, 6-4 in just under two hours Friday while Bautista Agut, the 2016 champion, defeated Robin Haase 6-7 (7), 7-6 (3), 7-6 (5) in a three-hour marathon.
Ferrer, who has slipped from a career-high No 3 to 38 has a 6-4 win record over the 13th ranked del Potro who struggled to get on top of Khachanov.
Both players will now turn their attention to next week's Australian Open in Melbourne, where Bautista Agut will play compatriot Fernando Verdasco in the first round.
The third set was similar, with no break-point opportunities until the 11th game when Bautista Agut broke del Potro to go ahead 6-5.
The final set remained with serve until Bautista Agut broke at 5-5 and then served for the match.
A red-hot favourite for the match, the world No.21 found valiant opposition in Haase, who recovered from a poor start to win the first set. "Juan Martin is a great champion, he's very tough to beat, and I played two unbelievable games in the last two games of the match". Every weapon in their armoury was on display, with Haase even switching his racquet from the right toleft hand to reach shots swinging away down the backhand side.Del Potro and Ferrer's rallies were generally shorter as they slugged it out from the base line.
"I have many good things to celebrate - of course, when you lose in a final, it's not happiness, but the tennis life continues". "I tried to have Juan Martin moving around the court". "I couldn't play any better, but Roberto did well at the end of the match, and I made some mistakes". "The end was unbelievable when I saw the ball in I went insane, I was so happy". He again saved a break point before winning the set in 50 minutes.