Already on the brink of bowing out owing to last week's 3-0 horror show at Anfield, Jurgen Klopp's men prevailed on the night thanks to an early Mohamed Salah penalty, but they otherwise lacked penetration and were sent packing with a whimper.
As a result, barring a sensational change of heart, Klopp has taken charge of Liverpool in European competition for the last time, but the German could still depart with two domestic medals around his neck.
The EFL Cup winners will only be fighting for Premier League glory between now and the end of the season, resuming their quest for top-flight stardom away to Fulham on Sunday with a two-point gap to make up to leaders Manchester City.
Salah wastes gilt-edged chance after powerful penalty
The Liverpool XI tasked with masterminding another epic European turnaround featured three changes from the weekend's loss to Crystal Palace, as Cody Gakpo, Dominik Szoboszlai and Trent Alexander-Arnold returned to the fold.
Within just seven minutes of the match, the latter had already returned to his assisting ways - albeit in unconventional circumstances - as his cross struck the outstretched arm of Matteo Ruggeri in the Atalanta box.
Liverpool's all-time leading European scorer Mohamed Salah stepped up and made no mistake with an emphatic penalty, before immediately carrying the ball back to the centre circle as a gung-ho Liverpool achieved lift-off in their comeback mission.
Jurgen Klopp's men were nearly back at square one in the 14th minute, though, had it not been for Alisson Becker, who clawed Virgil van Dijk's sliced clearance away from danger after the Dutchman made a meal of dealing with Teun Koopmeiners's cross; the offside flag soon went up anyway.
The relentless Liverpool pressure did not let up, but Salah failed to replicate his clinical ways from the spot in the 39th minute, spooning a lob over the head of Juan Musso but wide of the post after Gakpo's clever ball over the top.
Koopmeiners had the ball in the back of the net just two minutes later, but Atalanta's celebrations were cut short by the offside flag, and Liverpool still had the steepest of hills to climb in the second period despite their slender lead.
Leggy Liverpool lose intensity in second half
As a cutting edge still eluded Klopp's side, Gian Piero Gasperini's men found a couple of openings in the final third early in the second half, but Alisson Becker was only called into simple stops from Koopmeiners and Ederson.
The Reds' hopes of pulling off a mammoth comeback faded with every passing minute, though, and Klopp made the bold call to bring Salah off as part of a triple change just past the hour mark, introducing Diogo Jota, Darwin Nunez and Harvey Elliott into the action as Atalanta upped the ante.
After expending so much energy in the opening 45 minutes, Klopp's men cut jaded figures as the game entered its closing stages, seeing their ineffective attacks easily snuffed out by La Dea and also having to do their fair share of defending.
Teenage striker Jayden Danns was thrown on for the final 10 in one last throw of the dice, but the 18-year-old's introduction could now spark new life into Liverpool, and Gasperini could afford a beaming smile one minute before the referee's whistle sealed Liverpool's fate.
Klopp's crop amassed just 0.11 Expected Goals (xG) from two shots in the second half, while a firework display lit up the Gewiss Stadium as Atalanta hugs flowed on the field at full time.