The EC's decision came days after it had banned the two leaders from campaigning in Uttar Pradesh during the ongoing Lok Sabha elections.
While censuring the two, the EC also condemned their statements after going through their responses to the show cause notices issued to them.
The ban imposed on the two politicians will continue.
"Whereas, the Commission has considered the aforesaid reply dated April 11, 2014 carefully and has again seen the video recording of his (Khan's) impugned speeches and is convinced that he has made highly provocative speeches which have the impact of aggravating existing differences or create mutual hatred between different communities...
"...Commission, without prejudice to any other order/notice issued or to be issued in the matter relating to MCC violation to him, hereby condemns the impugned statements made by him during election meetings...and censures Shri Azam Khan for the above said misconduct," the EC order on Azam Khan said.
The poll body made similar observations against Shah in a separate order after going through his response.
Shah had landed in a major controversy for his remarks that the upcoming general election was an opportunity to seek "revenge for the insult" inflicted during the riots in Muzaffarnagar in Uttar Pradesh last year.
EC took cognisance of his remarks made in Shamli, Bijnore and Muzaffarnagar in West UP.
Khan, a UP Minister and a senior Samajwadi Party leader, had hit the headlines with his controversial statement that it was Muslim soldiers who had won the Kargil war for the country in 1999 and that no Hindu soldier had died.
The EC order took note of his remarks made in Ghaziabad and Rampur.
last week, the EC had cracked the whip on Shah and Khan by banning them from holding public meetings, processions or roadshows in Uttar Pradesh and asked authorities to initiate criminal proceedings against them.
The EC had also directed the Chief Secretary to ensure that no act of commission or omission is resorted to by BJP leader Amit Shah and UP Minister Azam Khan that can affect public tranquillity and law and order.
The EC was also critical of the role of Samajwadi Party government in the state for "soft-pedalling" on registration of FIRs against Khan and not dealing with the sensitive issue with alacrity.
The EC had taken the decision even before the two responded to its show cause notice as it wanted to check them from further vitiating the election atmosphere in UP.
The poll body had directed the authorities to take all preventive measures against Shah and Khan under relevant provisions of CrPC to ensure that no act of commission or omission is resorted to by them which has the effect of prejudicially affecting public tranquillity and law and order.