The Singapore side picked up their first win since April 15 with two early goals in the space of five minutes
First-half goals from Khairul Amri and Zulfahmi Ariffin were enough to see off the Malaysian Super League strugglers, although a late strike from Rezal Zambery Yahya led to a nervy end.
The home side started strongly and were clearly in search of three points, with coach Fandi Ahmad having promised a win after the mid-week defeat to Johor Darul Takzim.
Shahfiq Ghani who had only made cameo appearances in recent matches was given a starting berth, playing behind lone striker Khairul Amri.
Afiq Yunos and Madhu Mohana, who picked up cautions in their last match were both suspended for tonight's match, but their absence paved the way for the return of Baihakki Khaizan who was playing his first home match since his return.
The addition of Shahfiq proved to be a crucial move, as the LionsXII opened their scoring following the forward's pinpoint corner-kick.
His 16th minute cross was headed home from close range by an unmarker Khairul Amri who registered his seventh goal of the season in the process.
However, LionsXII should have had the lead just moments earlier when a Shahfiq pass found Gabriel Quak behind the ATM defence, but the winger scuffed his chance inside the penalty box leaving the home side waiting for a breakthrough.
Five minutes after scoring the opener, Khairul Amri turned provider, this time holding off his marker to lay off the ball to Zulfahmi, who strode past one ATM defender and wrongfooted another to smash the ball to the top corner of the net from close to the byline.
Two goals up and brimming with confidence the home side went in search of more, while ATM made a double change at the half-hour mark to rescue a game they were fast losing control of.
Faris Ramli and Quak both came close before Izwan Mahbud found himself with work to do, brilliantly palming away Juan Arostegui's close range effort.
It was then his ATM counterpart's time to put his talents on display 10 minutes before the break. Khairul Amri was denied inside the six-yard box by Syed Adney and then seconds later the Malaysian goalkeeper acrobatically diverted Zulfahmi's well-timed volley.
LionsXII almost extended their lead two minutes after the restart but a scuffed shot from Faris cannoned off the framework with the goalkeeper and defence looking beaten.
But the game started to lag in pace as the LionsXII failed to create more chances to add to their lead.
It was at the 78th minute that the match came back to life with Rezal Zambery scoring against the run of play and with the home side looking off pace.
The ATM captain collected a well-worked one-two and burst into the penalty box before firing past Izwan to cut the LionsXII's lead.
However the goal failed to ignite a late charge from the visitors who still could not conjure up enough to threaten Fandi Ahmad's side.
LionsXII hung on to a crucial 2-1 win, their first since mid-April when they overcame Pahang FA 4-1.
They next face Kelantan FA away on June 10.