Prajapati, a minister who has been booked on the directions of the Supreme Court, however, left the dais when Akhilesh arrived.
Party sources said the Chief Minister did not want to share stage with Prajapati and had asked the organisers of the rally to ensure that he was not present when he spoke.
Akhilesh, in his election rally at Gauriganj in Amethi district, did not make any reference to his controversial cabinet colleague during his entire speech.
Opposition parties have made it a big issue with BJP targeting Priyanka Gandhi Vadra over her poll campaign in Rae Bareli for the Congress-SP alliance, saying it was unfortunate that she was seeking votes for those accused of "rape and murder".
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Prime Minister Narendra Modi only yesterday raked up the Prajapati issue, saying at an election rally that the Supreme Court had to intervene to get the minister booked in an alleged rape case.
Amethi is the Gandhi family pocket borough and is represented by Congress vice-president Rahul Gandhi in the Lok Sabha, while neighbouring Rae Bareli is represented by party chief and Rahul's mother Sonia Gandhi in the Lower House of Parliament.
Steering clear of the controversy, Akhilesh exuded confidence that the SP-Congress alliance would form the next government in Uttar Pradesh.
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Prajapati was seen wiping his tears just before leaving the stage.
"They (BJP) made you stand in long queues outside. Now time has come for you to once again stand in long queues and give a befitting reply to the BJP," he told the gathering in reference to demonetisation decision.
He also said the people of the country have not been able to understand the Prime Minister's 'Mann ki Baat', referring to his monthly radio address to the nation.