Sock had complained of suffering flu-like symptoms when he stunned four-times champion and world number eight David Ferrer in the semi-finals on Friday and the 23-year-old American was unable to get around the court to make a contest of the final.
Bautista Agut, whose previous titles came in 2014 when he was voted most improved player on the ATP tour, had reached the title-decider by coming from a set down to upset French second seed Jo Wilfried Tsonga.
After starting the match with two double faults, the 26-year-old Spaniard picked up where he left off against world number 10 Tsonga and raced through the first set in 20 minutes of one-sided tennis against the clearly ailing Sock.
The American had lost the opening set in his quarter-final against Kevin Anderson, and in his semi against top seed Ferrer, but there was no way back on Saturday and he called it quits after losing his first service game in the second stanza.
Bautista Agut, ranked 25th in the world, will open his fifth Australian Open main draw campaign on Monday or Tuesday against Slovakia's Martin Klizan, who withdrew from this week's Sydney International with a shoulder injury.
Sock, who was looking for his second career title, will be hoping to play his opening round match at Melbourne Park against a qualifier on Tuesday to give him time to recover from the virus.
(Reporting by Nick Mulvenney in Sydney; Editing by Peter Rutherford)
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