The Blues needed a win to guarantee top spot in Group C but found Atletico goalkeeper Jan Oblak in inspired form before Saul Niguez nodded in with an effort that looked like it might seal a win for Diego Simeone's side, themselves needing maximum points to have any chance of going through.
Roma beat Qarabag 1-0 in the Eternal City, however, to deny both teams here, eliminating Atletico and giving Antonio Conte cause for concern after his side could not add to Stefan Savic's own goal.
The latter sides would likely send panic through Stamford Bridge. PSG eliminated Chelsea in their last Champions League campaign in 2016, but the Blues have not played Barca since the semi-final win over the Catalans en route to the title in 2012.
Though Atletico are notoriously difficult to beat, Conte will be concerned after Chelsea failed to score with 17 shots on goal. Such wastefulness will not help the Italian finally leave an imprint on this competition come the new year.
Atletico started with the intensity of a team needing to win, but Fernando Torres' deflected effort and a lashed Thomas Partey shot cleared the bar in the sum of their efforts.
Lucas Hernandez was destroyer-in-chief whenever Eden Hazard took possession but the Frenchman earned a booking and a warning from referee Danny Makkelie for fouls on the Belgian, which curtailed the rough stuff and allowed Hazard greater room to operate.
Former Real Madrid man Alvaro Morata curled wide and twice tested Oblak, first off-balance from close range and then from an angle, but Hazard ought to have done better when he scuffed harmlessly from 15 yards when picked out well by Tiemoue Bakayoko.
Oblak was again put to work by Davide Zappacosta's low drive as Chelsea continued to dominate to the break and the Blues began the second half with Morata, Hazard and Andreas Christensen going close before Atletico suddenly pounced.
Filipe Luis hit the post from 25 yards, but news soon filtered through that Roma had taken the lead, which led to stern celebrations from Simeone when Saul peeled off Bakayoko to convert Torres' flick-on inside the six-yard box.
390 - Saúl Ñíguez's goal was Atletico's first away from home in the Champions League in six and a half hours of football (390 minutes), since the Spaniard scored at Leicester in April. Call.— OptaJoe (@OptaJoe) December 5, 2017
Cesc Fabregas routinely found space right up on the Atletico byline and one such raid ought to have been converted by Christensen, but the defender bundled wide from inches out.
The goal finally arrived 15 minutes from the end, Hazard a predictable source as his fizzing cross was too quick for Savic, whose unorganised feet directed the ball high past Oblak.
The goalkeeper sprung from his line barely a minute later to smother Morata one-on-one and an unmarked Willian blazed over to leave Conte chewing over a likely heavyweight contest in the first knockout round.
Key Opta stats:
- Since 2003-04, this is just the fourth time Chelsea have failed to finish top of their Champions League group (1st x10, 2nd x3 and 3rd x1).
- The Blues have lost just one of their last 41 Champions League group stage matches at Stamford Bridge (W30 D10) – a 1-2 loss against FC Basel in September 2013.
- Chelsea have also scored in 27 successive Champions League group stage home games – the last time they failed to score was in a 0-0 draw against Valencia in December 2007.
- The last time Atletico were knocked out of the Champions League group stage was in 2009-10 when they won the Europa League at the end of the season.