Jeje struck in 73rd and 88th minutes while the other goal scorers for Mohun Bagan were Sony Norde (48th), Dhanachandra Singh (58th) and Bikramjit Singh (82nd) after the two sides were locked goalless at the end of the first session at the Indira Gandhi Athletics Stadium.
Mohun Bagan's 14th title, the most by any club in the country in the prestigious tournament, will give them the right to play in the AFC Cup after they missed out on the I-League title this season. They won the title after a gap of eight years, since their triumph in 2008. For Aizawl, it was a case of so near yet so far as they failed to end their fairytale campaign with a title triumph.
Playing in their maiden Federation Cup after finishing eighth in the I-League (which they also qualified for the first time), the Aizawl side had beaten I-League champions Bengaluru FC and Sporting Clube de Goa en route to the final.
Mohun Bagan striker Glen Cornell missed a golden chance in the 34th minute as his strike off a Katsumi Yusa corner did not have enough power and Aizawl keeper Soram Poirei collected it easily.
Mohun Bagan returned a completely different side in the second half and pumped in five goals as Aizawl surrendered meekly to their far superior opponents.
The floodgates were opened three minutes after resumption with Norde slotting the ball home after a Bikramjit Singh and Jeje Lalpheklua build-up.
Dhanachandra Singh made it 2-0 as he nodded home, connecting a Katsumi corner at the far post. Jeje made himself enter the scoresheet with a curling shot after a fine back-heel by Cornell in the 73rd minute.
Nine minutes later, Norde dodged past a host of Aizawl defenders from the left and squared the ball for Bikramjit to place it into the empty net.
Two minutes from regulation time, Jeje struck his second goal as he tapped the ball into the Aizawl net from an Azharuddin Mullick pass to complete the route.