Without the services of top scorer Jean-Emmanuel Owona due to suspension, Negri went behind to rock bottom Kuala Lumpur, Afiq Azmi opening the scoring in the eighth minute at the Hang Jebat Stadium.
Undaunted, Negri, reigning Malaysia Cup champions and winners of this season's Charity Shield, hit back just five minutes later when Shakir Ali grabbed the equaliser.
Azraai Khor Abdullah's charges then ensured all three points courtesy of Shahurain Abu Samah's effort 13 minutes from.
Negri are now five points behind league leaders Kelantan who play host to Felda United on Saturday, while Kuala Lumpur remain rooted to the bottom of the table, with just one point to their name.
In Friday's other match, Ghanian import Mohamded Hamidan was the star for Kedah as they breezed past Perak 3-0 at the Darulaman Stadium in Alor Setar.
Kedah, who reaced the semi-finals of the Malaysia FA Cup this week thanks to an aggregate victory over T-Team, went ahead on 44 minutes, Hamidan converting the ever impressive Badrol Bakhtiar's corner.
Perak's Syazwan Roslan then put through his own goal, before Hamidan lashed home a long-range screamer in the 83rd minute.
The win lifts Kedah to ninth. Perak remain in seventh.