Jankovic's buildup to Flushing Meadows has not inspired hope that the Serb will be making a return to the final this year with her play on the North American hardcourts falling flat and concern over a nagging ankle injury mounting.
"I don't have any pain anymore, I just need to work hard on the practice court and work on getting better," Jankovic, runner-up at the 2008 US Open, told reporters.
"I'm not where I would like to be, my game is not there.
"I have a week-and-a-half before the U.S. Open so hopefully I can prepare and play better there," she added.
The lost marked the third consecutive hardcourt event that the world number three has made an early exit, having also fallen at the first hurdle in San Diego to Russian Alisa Kleybanova.
The 25-year-old from Belgrade won her opening match last week in Cincinnati but then was dispatched in straight sets by Akgul Amanmuradova of Uzbekistan in yet another upset.
Prior to her injury, Jankovic had been enjoying a solid season highlighted by a win at Indian Wells.
Her problems began after Wimbledon when she was forced to retire from a tournament in Slovenia.
BENESOVA FEARLESS
Benesova, who had never won a match on Canadian hardcourts in two previous visits and had won only two matches on hardcourts this season, would not be intimidated by the former world number one.
Jankovic, who showed no signs of an injured ankle, had looked in control, serving for the first set at 5-3.
But the 27-year-old Czech broke the Serb to get back on serve, forcing the set to a tiebreak, which she dominated 7-3.
Benesova stepped up the pressure in the second set, breaking Jankovic at the first opportunity on her way to a 3-0 lead.
Jankovic offered a brief fight back with a break in the fifth game but Benesova would not buckle, breaking back to go up 5-3 and serving out the match.
"I just didn't play well, I wasn't on my game," said Jankovic.
"I made a lot errors and I didn't feel like myself out there. "I haven't been playing well the last couple of tournaments because I was just coming back from the injury.
"I didn't really feel like a top five player out there. My game hasn't been at the top level for the last couple of tournaments," she added.
In other action, Wimbledon finalist and eighth seed Vera Zvonareva led a Russian charge into the second round with 6-1, 6-2 demolition of Kazakhstan's Yaroslava Shvedova.
Svetlana Kuznetsova, the first Russian woman to win the U.S. Open, flashed her hardcourt pedigree dispatching Anastasia Pavlyuchenkova 7-5, 4-6, 6-1 as six Russians made it safely through.
Aside from Jankovic, it was a good day for the seeds, with number 10 Victoria Azarenka of Belarus crushing Ukraine's Kateryna Bondarenko 6-1, 6-1, and Italian 15th seed Flavia Pennetta rolling past Slovakia's Daniela Hantuchova 6-0, 7-5.
Sania-Monica shock Wimbledon champs in Cincinnati
Jankovic, Wozniacki upset in Cincinnati
Pennetta knocks out third seed Jankovic
Radwanska sets up Kuznetsova final at San Diego
Zimonjic-Srebotnik win French Open mixed doubles