He called it "defamatory" and said the contracts were illegal campaign financing requiring action from electoral authorities.
Bolsonaro said in an online video that he had no knowledge of such activity and called on any supporters doing so to stop.
According to a report Thursday in local newspaper Folha de Sao Paulo, several digital marketing firms have leveraged WhatsApp's encrypted services to circulate unregistered political propaganda, most of it attacking Haddad. None of the companies mentioned immediately responded to requests to confirm they had received the "cease and desist" letters.
WhatsApp banned hundreds of thousands of accounts in Brazil as the Facebook Inc. messaging service struggles to contain political shenanigans ahead of a runoff election in Latin America's largest country.
WhatsApp is immensely popular in Brazil, which is home to almost one in 10 users worldwide, but it has come under scrutiny during this election as concerns grow about whether false or manipulated messages are influencing voters.
WhatsApp said in a statement that it was taking the allegation seriously.
Numerous fakes portray Haddad as a communist whose Workers' Party would turn Brazil into another Cuba, convert children to homosexuality and rig voting machines. Chairwoman Gleisi Hoffmann said she feared there would not be a timely response to avert the false news wave before the runoff. "The court will treat this suit as if we were in normal times, so I am very anxious".
Later on Friday, Brazil's top electoral court TSE approved opening a probe into the case.
Bolsonaro, a seven-term congressman from a tiny party, had little access to public campaign funding or TV advertising but his grassroots campaign and outsized presence on social media helped him win 46 per cent of votes, almost foregoing a run-off.
One of Brazil's top newspapers on Thursday claimed Brazilian entrepreneurs were bankrolling a multimillion-dollar campaign created to boost Jair Bolsonaro by inundating WhatsApp users with messages undermining his leftist rival Fernando Haddad.
"There is no limit to the persecution!"
WhatsApp confirmed that it had blocked Flavio Bolsonaro for "spam behavior" and reasons unconnected to the Folha report. Flavio Bolsonaro tweeted Friday when he initially revealed his account had been blocked. The opposition claims the campaigns are being bankrolled by pro-Bolsonaro businessmen at the candidate's behest.
Brazil's federal police also opened an investigation into allegations of spam message campaigns on WhatsApp related to the election.