The petitioner accused Shaji of securing a win in the Assembly polls in 2016 by a margin of 2,287 votes using corrupt practices.
Left Democratic Front (LDF) candidate M V Nikesh Kumar, who had contested the polls against Shaji, had moved the HC alleging he used corrupt practices to secure a win in the 2016 Kerala Assembly elections.
News agency PTI reports, Justice P D Rajan, who was hearing the case, directed the Kerala Assembly Speaker and Election Commission to take action against Shaji on its order.
The petitioner claimed that Shaji used religion to secure a win in the polls — a violation of the Representation of People Act.
Kumar said Shaji, a Muslim, appealed to the electorate to vote for him on grounds of his religion and urged people not to vote for those who did not believe in Islam.
Shaji had won the elections by a margin of 2,297 votes. IUML is an ally of the Congress-led Opposition United Democratic Front (UDF) in Kerala.
IUML, reacting to the verdict, said it would consider appealing against the HC order after reading the judgement.