By ESPNSTAR.com staff
On-loan striker Afiq Azmi opened the scoring for the Red Warriors in the 16th minute but Marlon Alex James equalised for the Armed Forces in the 33rd minute, although Norshahrul Idlan Talaha restored his side's lead three minutes later.
However, ATM pulled level again two minutes later when James grabbed his second, and they were ahead by halftime after Hairuddin Omar fired home in the 43rd minute.
Despite Kelantan's best efforts, they struggled to break down the visitors' resilient defence until the 87th minute, when Norfarhan Mohamad found the back of the net, and the comeback was completed shortly after when Nurul Azwan Roya grabbed a 89th-minute winner.
Nonetheless, both sides remain favourites to progress to the quarter-finals as they are currently three points ahead of Terengganu and Kedah, who played out a 1-1 draw at the Sultan Ismail Nasiruddin Shah Stadium.
Pahang became the first team to advance to the knockout round after beating Sarawak 3-2 at the Sarawak State Stadium.
The hosts went in front after 17 minutes through Rasyid Aya and although Maycon Carvalho equalised for Pahang ten minutes later, Joel Epalle netted four minutes before the break to give the Crocs the lead at the break.
However, Malaysia international Azamuddin Akil put in an inspired display in the second 45 to grab his side all three points by making it 2-2 in the 63rd minute, before grabbing the winner 11 minutes later.
Selangor continued their recent resurgence by beating T-Team 2-1, courtesy of a first-half double from Croatian striker Bosko Balaban.
Jean-Emmanuel Effa Owona scored the only goal of the game in first-half injury-time to hand Negri Sembilan a 1-0 win at Perak, a result which was enough to see them move three points clear at the top of Group C after closest challengers Sime Darby and Felda United drew 3-3.
Finally, LIONSXII stayed top of Group A after recording a hard-fought 1-0 win over Johor, which came courtesy of Khairul Amri's second-minute strike, while Johor FC remain behind the leaders on goal difference after beating PKNS 2-1.
Saturday's Malaysia Cup Results
LIONSXII 1-0 Johor
Johor FC 2-1 PKNS FC
Kelantan 4-3 ATM
Terengganu 1-1 Kedah
Perak 0-1 Negri Sembilan
Sime Darby 3-3 Felda United
Sarawak 2-3 Pahang
Selangor 2-1 T-Team