On a drying Spa-Francorchamps circuit, timing the final flyer to perfection was of the essence, with Red Bull's Max Verstappen pipping McLaren prodigy Oscar Piastri to the top of the timesheets.
Mercedes appeared to have misjudged its drivers' positioning to start the final lap, with Russell hindering Hamilton after locking up his tyres into Turn 1.
Hamilton then passed Russell on the Kemmel straight, but not before he had to back out of the throttle and see his final lap ruined as well as Russell's.
It meant Hamilton was bumped down to seventh, with Russell abandoning his lap and starting Saturday afternoon's sprint race from 10th.
Afterwards Russell blamed poor communication for his close encounter with Hamilton, while also admitting he had been off his game throughout the session.
"It was a total mess from start to finish to be honest," Russel told F1 TV.
"I was surprised I got to Q3 because [there were] so many mistakes from my side and a bit of miscommunication at the end. I was too close to the car in front, Lewis was too close to me.
"We thought we weren't going to make the lap because the clock was running down. But there was definitely more time on the clock than we foresaw, because I think Max was the last car to cross the line.
Russell added: "It was a total mess this weekend, really, not going to plan. I hope we can make a bit of a recovery.
"I'm definitely confident we can be quicker in the race, but so far single lap qualifying has been rubbish."
Hamilton felt he would have qualified on the front row if Russell hadn't gotten in his way.
"Not happy about it, obviously," Hamilton added. "It was looking great; I had that first lap that put me first.
"I reckon I could have been first or second in that session, communication was pretty poor. We got to the last corner and there were seven cars trundling around.
"We were led to believe we had no more time left but it turned out we had plenty of time. And then with George, it is what it is. It doesn't really matter."
Hamilton was more upbeat about Mercedes' overall car performance, the seven-time world champion lining up in third on Sunday's grand prix grid.
"I feel great in the car in all conditions," he explained.
"A little bit slower than the Red Bulls in the middle sector, but none of us have driven on heavier fuel, so I'm excited that it's dry today so hopefully we can have a good race."
