The 22-year-old, deputising for Lewis Hamilton following the seven-time world champion's positive coronavirus test, missed out on a fairy-tale pole position by an agonising 0.026 seconds at this 2.2-mile Bahraini venue.
Russell, a Williams driver by day, has been handed the keys to the fastest car in Formula One history after Hamilton returned a positive Covid-19 test result on Monday.
Hamilton's Mercedes boss Toto Wolff said the 35-year-old "is in bed", and "not feeling great" as he isolates in his hotel room.
Speaking on Saturday night, Wolff said: "I last spoke to Lewis on Thursday and we have been texting every single day. I try to leave him in peace because Covid-19 is no fun. I think he is OK."
Hamilton has dominated this year, winning 11 of the 15 rounds, but his enforced absence – the first Formula One weekend staged without the record-breaking Briton since the season-ending 2006 Brazilian Grand Prix – has provided a glimpse of what life might look like after he calls time on his career.
And Russell, who could yet team up with Hamilton at Mercedes in a mouth-watering all-British line-up the year after next, has impressed in his first, very public audition.
"It has been really tough to jump in last minute, learn a new car, work with new engineers, understand how to make this car go fast because it is a completely different ball game," said Russell.
"Obviously I'm gutted to miss out on pole by 20 milliseconds.
"Being so close to pole makes it slightly more frustrating, but if you told me four days ago I would qualify second, I'd thought you'd be pulling my pants down. I have to be pretty pleased."
Russell revealed Hamilton sent him a message on Friday night. "He wished me well and said to look after his car," added the Briton. "So far so good."
Hamilton's £40million-a-year deal expires at the end of the month and Russell's mature performance might provide Wolff and Mercedes chairman Ola Kallenius with a prominent bargaining chip when it comes to discussing the terms of their star driver's new contract.
Russell has not scored a single career point, with a best finish of 11th in Mugello earlier this year. But he will start among the favourites to become only the fourth British driver to win a Formula One race this century in his 37th appearance on Sunday.
"I have been very relaxed this weekend," added Russell ahead of the sport's penultimate round of the year. "When I was waiting for confirmation to get the drive I was incredibly anxious, but as soon as I got the confirmation I saw it as a great opportunity and I was pretty chilled.
"Toto just said: 'Go out and enjoy it. There are zero expectations. We are not expecting anything from you and if you qualify in the top six, that's fine, you can still get a podium from there.'
"Tomorrow, I am going to leave satisfied or disappointed dependant on how I feel I did – whether that is a win, or third, or fifth or whatever. I am going in with an open mind. Just balls out. Everything I have got."
The sport is back in Bahrain for a second race in as many Sundays, but a new configuration of the Sakhir track is being used.
Registering at just 2.2 miles and effectively featuring only six corners, Bottas' 53.37 second lap was the lowest since Niki Lauda put his Ferrari on pole for the French Grand Prix in Dijon 36 years ago in 58.79 sec.
The 6ft 2in Russell will tackle 87 laps – the highest number for a grand prix in a quarter of a century – crammed into a cockpit designed for Hamilton's 5ft 7in frame.
Russell concluded: "It is going to be a long and fatiguing race because I am not comfortable in the car. I had ice on my shoulders last night to reduce some swelling on my knees and my toes, too. But when the car is so fast you forget about the pain."