PepsiCo said it alerted Coca-Cola after it received an e-mail from a man calling himself 'Dirk', offering "very detailed and confidential information" that only a few top Coca-Cola executives had seen.
The case is a warning to food and drink firms to be continuously on their guard against industrial espionage.
Video surveillance set up jointly by the FBI and Coca-Cola allegedly taped Joya Williams, an executive administrative assistant at Coke, stuffing files and a liquid container, believed to be a new product sample, into her bag.
The FBI said it believed Williams, 41, was passing information on to 'Dirk', who it revealed as 30-year-old Ibrahim Dimson, from Bronx in New York.
An undercover FBI agent allegedly met Dimson in the Hartsfield-Jackson International Airport, where Dimson handed over a brown bag containing classified Coca-Cola documents and a new product sample. He was paid an initial $30,000 (€23,500), with another $45,000 to be paid later.
The FBI claimed Dimson then left the airport with the third suspect, Edmund Duhaney, aged 43 and from Decatur, and that the two set up a joint bank account later that day.
The three suspects were due to appear before Atlanta magistrates on Thursday.
Coca-Cola later confirmed that Dimson had indeed gained access to 'valid trade secrets', and that the product sample involved was a genuine product under development.
PepsiCo, which recently overtook Coca-Cola in market value for the first time in 112 years of competition, was praised by US lawyer David Nahmias for alerting its arch-rival to the espionage.
"Theft of trade secrets will not be tolerated, not by the Justice Department and not even by competitors, as this case shows," he said.
The FBI has estimated that US firms lose a combined $100bn per year through industrial espionage, according to a report in this month's World Finance magazine.
The Coca-Cola case is, however, more of a traditional spy drama. Most analysts predict that internet hackers will be the main threat to companies' trade secrets in the future.
So-called cyber attacks have become much more sophisticated over the last year, according to a recent report by internet security group Counterpane & Messagelabs.
"Cyber attacks will cause greater damage to corporations in the coming years," warned Bruce Schneier, founder and chief technology officer at Counterpane. "We estimate that some malware with a modest infection rate could cost a small company $83,000 per year."