Having extended their unbeaten run to six games with a 1-1 draw at Chennaiyin Kolkata on Tuesday, Atletico saw things fall apart in Friday's 3-1 defeat to Pune City - their first loss of the tournament.
Atletico appeared to be on their way to three points against Chennaiyin when Spanish forward Luis Garcia struck his first goal of the season from the penalty spot in the 35th minute, and the hosts' misery was compounded by a red card for Shilton Pal.
However, the visitors were down to 10 themselves shortly after the restart when Jofre saw red and they were denied the win by Elano's spot-kick in the 90th-minute - his sixth goal of the season.
Three days later, Atletico had the chance to put that disappointment behind them but, on coach Antonio Lopez's return to the dugout following a ban for an altercation with FC Goa's Robert Pires, they were easily beaten by Pune.
Dudu Omagbemi opened the scoring for the visitors on 35 minutes with a towering header and experienced Greek midfielder Kostas Katsouranis doubled their lead 10 minutes into the second half.
Atletico threatened a late revival when Fikru Tefera halved the arrears from the penalty spot with six minutes remaining, but Davide Colomba secured Pune's win with an 89th-minute strike - lifting his side into third place.
Mumbai City moved into fourth place in the table with a 1-0 win over Delhi Dynamos, Nicolas Anelka netting his second goal for the club just before the hour.
Meanwhile, a Milagres Gonsalves strike gave Kerala Blasters a 1-0 victory against Goa, leaving the latter bottom of the table with just four points from six games.
