An Arda Turan strike in the 29th minute was enough to secure the Spanish club qualification with 10 points.
The Hoops have to beat Udinese in their last group fixture in Italy on December 15 to leapfrog the Italian club into second place and with a poor away record in Europe, their task is uphill to say the least.
Celtic had more than held their own against Atletico until the Turkey international picked up a Daniel Majstorovic clearance from Diego's corner 20 yards from goal and fired back in past Fraser Forster.
Substitute Gary Hooper, an interval replacement for Victor Wanyama, had the ball in the net after the break only to see it chalked off with an Anthony Stokes handball apparently the reason.
From the starting XI which thrashed St Mirren 5-0 at home in the Clydesdale Bank Premier League at the weekend, Hooper had surprisingly been dropped for midfielder Ki Sung-yueng.
Skipper Scott Brown and Mohamed Bangura returned from respective ankle and knee injuries but could only find places on the bench.
The dropping of Hooper, who scored a hat-trick against the Buddies, was perhaps with a view to Sunday's SPL game against Dundee United at Tannadice but it still perplexed the Parkhead crowd, which was seemingly affected by the unusual kick-off time of six o'clock.
With less than a minute gone, following an Atletico corner which Hoops defender Glenn Loovens originally headed clear, Eduardo Salvio headed wide of the target from close range.
Celtic asserted themselves on the game Ki's corner from the right was headed on by Majstorovic and Samaras' close-range flick drew a reaction save from Thibaut Courtois.
Samaras looked in the mood and after motoring down the left and into the Madrid box his cut back from the by-line was cleared by Atletico defender Filipe Luis, with the visiting defence looking as rocky as their Hoops counterparts.
As the driving rain and wind returned, lone striker Stokes took a James Forrest pass and did well to set up Samaras inside a crowded Atletico penalty box but the stretching Greece striker blazed over the bar.
Atletico were slick on the counter but it was from a corner that the Spanish club took the lead through Turan.
Diego's ball from the right was headed clear by Majstorovic only for the Turkey international quickly to drive powerfully back in from 20 yards.
Celtic's stand-in skipper Beram Kayal appeared to dip his head to allow the ball to fizz straight past Forster and into the net.
As the home side wobbled Salvio and Gabi had efforts which missed the target.
In the 37th minute Hoops left-back Joe Ledley had to be replaced by Charlie Mulgrew after picking up an injury which required him to be carried off on a stretcher up the tunnel.
Wanyama was replaced by Hooper for the start of the second half with the former Scunthorpe striker sent up to support Stokes, in what was a show of intent by Lennon.
Atletico, though, started as brightly as they had begun the first period and within two minutes of the restart Gabi had surged forward before sending a shot wide of the target from the edge of the box.
At the other end, moments later, Stokes linked up with Samaras before the Irishman's low drive was saved by Courtois down at his right-hand post.
Salvio again caused problems as the Parkhead defence made a hash of clearing their lines, getting past Majstorovic and Kayal before driving the ball past Forster and across the Hoops goal, finding no takers.
On the hour mark, with Celtic getting a foothold in the game again, Kayal latched onto a Loovens header from a Mulgrew free-kick and sent a volley just wide of the target.
Moments after Courtois made a great save under the bar from Ki's whipped free-kick at the expense of a corner, Hooper had the ball in the net from close range only to see the assistant referee with his flag raised.
Forster then fumbled a inswinging free-kick from Diego onto the bar and Celtic escaped but the Hoops keeper subsequently did better when he foiled Salvio's attempt to lob the ball over him 12 yards from goal.
Stokes was replaced by Brown in the 75th minute and the home side began pushing for the leveller, which, ultimately, failed to arrive.