Scottish striker Duffy continued with his ominous form as he found the target in the 16th and 32nd minutes, while the AIFF Player of the Year Jeje (28th and 77th) added to the tally on both sides of the break as Mohun Bagan toyed with the defence of the Punjab side.
Witn their third successive home wins this season, Bagan lead the I-League table with nine points.
Bolstered by the inclusion of their high-profile Haitian striker Sony Norde, who started along with Jeje, Mohun Bagan, with five changes, looked menacing right from the start.
Mohun Bagan now hit the road as they will face Goan outfit Churchill Brothers in their season's first away encounter January 21.
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Backed by a boisterous crowd who shouted every time he held the possession, Sony was in his elements and set up the opening goal from an awkward angle outside the box from the left before Duffy gave the lead with a perfectly-timed header.
Jeje then opened his account this season with another attacking play.
Two minutes later, Sony found himself in another dangerous move with Duffy getting his head onto it before being thwarted by Arashpreet Singh. The former East Bengal player Arashpreet Singh was solid in the defence but only to be let down by his colleagues.
Duffy brought up his second double with his right-footer when Katsumi Yusa set up a long ball from centre.
Minerva looked closest to reduce the margin after the changeover but luck eluded them when substitute Joel Sunday's shot hit the crosspiece in the 64th minute.