Jyoti Sharma, her paramour Sher Singh and Shailu, his accomplice, were arrested and sent to jail, SP city Shalesh Pandey said.
Jyoti's son Bhupendra was missing since June 1, 2014.
Police said Jyoti was in an illicit relation with her tenant Sher Singh and she saw her son Bhupendra as an obstacle to her relationship.
"Jyoti told her paramour to engage a contract killer to murder Bhupendra and she would pay Rs ten lakh for it," Pandey said.
Then they dumped the body and the pistol in an abandoned well nearby, he added.
The body has been recovered and pistol seized, Pandey said.