Both KL Felda and Kelantan went into Wednesday's encounter unbeaten after winning their opening two matches against the other two teams in Group C, Sarawak and Johor FC.
But it was the capital city club which took the honours after Ferderin Kadir gave them the lead in the 27th minute, before D. Saarvindran sealed the result by adding a second in the 67th minute.
On Tuesday, Johor had claimed a 1-0 away win over Sarawak thanks to a penalty from Eddy Helmi Abdul Manan to move third in Group C.
In Group A, Perak and Sabah moved joint-top on seven points after both recorded victories on Tuesday.
Perak took the lead against Kedah through Muhammad Syafiq Jamal in the 15th minute, and although Mohd Khyril Muhymeen Zambri equalised in the 34th minute, Mohd Failee Ghazali struck what turned out to be the winner just two minutes later.
Sabah meanwhile recorded a 3-1 over Johor FA thanks to a brace from Zainijam Marjan, after Mohd Azuwad Mohd Arip had earlier cancelled out Radzi Mohd Hussin's ninth-minute opener.
Tuesday's action in Group B saw Negeri Sembilan record a narrow 1-0 win over Terengganu thanks to Shahurain Abu Samah strike, while Selangor PNKS beat KL Sime Darby by the same scoreline courtesy of Rajesh Perumal's ninth-minute effort.
In Group D, Kuala Lumpur stayed top of the table after a 0-0 draw with Selangor, although their lead is now just a solitary point after T-Team hammered PDRM to move second on six points.
Wednesday's Malaysia Cup Results
KL Felda United 2-0 Kelantan
Tuesday's Malaysia Cup Results
Perak 2-1 Kedah
Johor FA 1-3 Sabah
Negeri Sembilan 1-0 Terengganu
PKNS 1-0 Sime Darby FC
Sarawak 0-1 Johor FC
Kuala Lumpur 0-0 Selangor
T-Team 4-0 PDRM FC