Captaining Bayern Munich in the Champions League for the first time, Harry Kane converted a penalty with 25 minutes played and added another goal early in the second-half.
Nikola Krstovic earned a point for Atalanta by scoring in the 82nd minute at the San Siro, cancelling out Pio Esposito's angled drive.
Reeling from their six-goal mauling at the hands of Champions League heavyweights Bayern Munich, Atalanta take the short trip to Serie A leaders Inter Milan on Saturday trying to boost their waning top-four hopes.
Bayern Munich put one foot in the Champions League quarter-finals on Tuesday by sweeping aside Atalanta 6-1 in a powerful demonstration of why the German giants are one of the favourites to win the competition.
Lazio and Atalanta traded four second-half goals in a 2-2 draw in the first leg of the Italian Cup semifinals Wednesday.
Vinicius Junior scored and then alleged he had been racially abused during Real Madrid's 1-0 win away to Benfica in the first leg of their Champions League play-off tie on Tuesday, while Paris Saint-Germain came from two goals down to beat Monaco 3-2.
Atalanta beat Juventus 3-0 on Thursday to reach the Italian Cup semi-finals thanks to goals from Gianluca Scamacca, Kamaldeen Sulemana and Mario Pasalic.
Atletico Madrid said they have agreed a deal with Atalanta to sign Ademola Lookman on Sunday.
Inter Milan stayed at the Serie A summit on Sunday after beating Atalanta 1-0 to maintain their slender lead over local rivals AC Milan.
Enzo Maresca admitted he was "worried" by Chelsea's slump after Atalanta's 2-1 victory in the Champions League extended the Blues' winless run to four matches on Tuesday.
Cole Palmer will miss Chelsea's Champions League clash with Atalanta on Tuesday as boss Enzo Maresca tries to keep the injury-plagued forward fresh.
Croatian Ivan Juric has been sacked as coach of Atalanta after back-to-back Serie A defeats left them in the bottom half of the table, the club announced on Monday.
Napoli lead the Serie A pack with a perfect 12 points from their first four matches of the league campaign.
Khvicha Kvaratskhelia scored a superb goal as Paris Saint-Germain began the defence of their Champions League crown with a comprehensive 4-0 win over Atalanta.
Gian Piero Gasperini is set to join Roma on a three-year contract with a net salary of five million euros a season as the capital club try to re-establish themselves in the Serie A top four.
Atalanta qualified for the Champions League on Monday by beating Roma 2-1 and mathematically securing a place in Serie A's top four.
Atalanta were defeated 1-0 by fellow Champions League hopefuls Lazio.
Lautaro Martinez is gunning for the treble after scoring in Inter Milan's 2-0 win at Atalanta which moved the Italian champions three points clear at the top of Serie A.