Gonzalez's second-round defeat ended his chance of qualifying for the year-end Masters Cup later this month.
Also bidding to clinch his place in the Shanghai tournament was sixth seed Tommy Robredo of Spain, who beat Frenchman Sebastien Grosjean 3-6, 7-5, 6-4.
Grosjean, the 2001 champion, led 5-2 in the second set and twice served for the match before bowing out.
Gonzalez had his chances against world number 42 Benneteau. The fifth-seeded Chilean led 3-0 in the third set, with two breaks of serve, before his opponent staged a fighting comeback.
Czech Tomas Berdych started the defence of his title with a 6-7, 6-4, 6-2 win over Belgian Olivier Rochus but nonetheless dropped out of the race for Shanghai.
Berdych, who surprised the favourites to win the indoor event in 2005, is seeded eighth this year
TOUGH START
"It was a very tough start and I'm happy I've made it," Berdych told reporters.
"I like it here but I'm not putting any extra pressure on myself just because I won last year."
The Czech cannot now qualify for the Masters Cup after American seventh seed James Blake ousted Frenchman Arnaud Clement 6-4, 3-6, 6-4.
Finn Jarkko Nieminen, seeded 14th, triumphed 6-3, 6-4 over Italian qualifier Daniele Bracciali.
In one of the day's most exciting contests, France's Paul-Henri Mathieu knocked out Serbian 12th seed Novak Djokovic 7-6, 7-6.
British number one Andy Murray, seeded 13th, beat Argentine baseliner Juan Ignacio Chela 7-5, 6-0.
A string of high-profile withdrawals has left the tournament without five of the world's top six players.