By Gabriel Tan
Following a goalless first half, D. Christie Jayaseelan put the hosts ahead ten minutes after the break, before Bruno Martelotto doubled their lead six minutes later when he fired home from close range.
Negri substitute Firdaus Azizul then pulled one back in the 73rd minute after a Farizal Harun clearance smashed off his back and into the back of the net, but ATM captain restored his side's two-goal lead seven minutes later when he curled home a sublime strike.
Still, the visitors refused to give up and grabbed another a minute from time when Shakir Ali scored with a terrific acrobatic volley, ensuring there will be plenty to play for when both sides meet again in Tuesday's second leg.
In an enthralling encounter that saw both sides create a plethora of chances, the Deer were the first to create a real opportunity early on when K. Thanaraj found space inside the area and fired in a low drive that came back off the far post. The rebound fell straight back to the on-loan winger but he was unable to capitalise, sending the follow-up volley way over.
Negri then had the woodwork to thank in the 22nd minute when Aidil Zafuan picked up possession on the edge of the area and let fly with a vicious effort, only to see it clip the post and go wide with Farizal Marlias beaten all ends up.
Right on the half-hour mark, Marlon Alex James, who had netted 21 goals in the Premier League campaign, wasted a good chance when he blazed over unmarked from 12 yards out after a good flick on by Hairuddin, before Farizal Marlias did well to smother at his feet eight minutes later, after he looked set to latch onto an incisive through-pass by Martelotto.
Six minutes before the break, Jean-Emmanuel Effa Owona was also guilty of improvidence when he sent a free header off target after being picked out inside the box by a lovely cross from Khairul Izuan down the right.
James, who was giving Deer centre-back Marian Farbak all sorts of problems, then came close in the 54th minute when he attempted a bicycle-kick that was just wide, but a minute later the Armed Forces were not to be denied.
After breaking down the right and into the box, Zaquan Adha appeared to have wasted a decent opening when he scuffed a shot in a one-on-one situation with Farizal Marlias, but the ball trickled to Christie, who calmly cut inside Rashid Mamud and drilled a low shot into the back of the net.
Zaquan then went on another excellent run down the right on the hour mark and looked set to pick out James, who was waiting unmarked inside the six-yard box, only for Azmeer Yusof to dispossess him with a perfectly-timed sliding tackle.
Nonetheless, Azmeer's intervention merely delayed the inevitable as ATM got their second a minute later, when Azmi Muslim picked out James inside the area with a neat pass, who in turn laid the ball back to Martelotto. Despite having a sea of defenders in front of him, the Argentinean kept his composure and skilfully glided past Rashid and Farbak, before clinically sending a shot past Farizal Marlias' despairing dive.
However, the visitors were handed a lifeline in the 72nd minute when a comical error from Farizal Harun saw him inexplicably send a clearance straight at Firdaus despite being under no real pressure, leaving him watching on in horror as the ball looped over him and into the unguarded net.
By now, the game had really opened up and seven minutes later, ATM grabbed their third when Farbak, who was trying to recover after seeing James burst past him, attempted a tackle but only succeeded in prodding the ball to Hairuddin, who proceeded to score with an exquisite curler into the top corner.
Armed Forces coach B. Sathianathan would likely have viewed a two-goal aggregate lead as a fair result to take to Paroi for the second leg, but a minute from time, his side were stunned as Negri pulled another back thanks to a fantastic strike by Shakir, who had come on for the ineffective Khairul.
Seconds after fellow substitute Norismaidham Ismail dispossessed Martelotto on the edge of the area and sent a ferocious volley against the crossbar, the Malaysia international met the rebound with an acrobatic volley that arrowed straight into the bottom corner.
There was still time for one final chance for Negri to cap off an impressive comeback and force a draw when S. Kunanlan floated in an excellent cross into the box in the fourth minute of injury-time. Effa Owona rose highest and met the delivery with a powerful header that looked destined for the bottom corner, only to see Farizal Harun make amends for his earlier error with a smart reaction save.
But despite ultimately ending up on the losing side despite a valiant effort, Azraai Khor Abdullah's men will be confident in their ability to overturn the deficit in four days' time.
ATM: Farizal Harun, Azmi Muslim, Aidil Zafuan, Fitri Omar (K. Reuben 40'), Irwan Fadzli Idrus, Rezal Zambery, Hairuddin Omar, Zaquan Adha (Venice Elphi 82'), Bruno Martelotto, D. Christie Jayaseelan, Marlon Alex James.
Negri Sembilan: Farizal Marlias, S. Kunanlan, Marian Farbak, Shukor Adan, Azmeer Yusof, Shahurain Abu Samah, Rashid Mamud, Idris Abdul Karim (Norismaidham Ismail 75'), K. Thanaraj (Firdaus Azizul 46'), Khairul Izuan (Shakir Ali 66'), Jean-Emmanuel Effa Owona.