IEBC declared independent candidate, Feisal Bader, Msambweni MP-elect.
Mr Bader garnered 15,251 votes against ODM's candidate Omar Boga who got 10, 444 votes.
On Wednesday, Feisal Abdallah, who was accompanied by Jubilee MPs allied to DP William Ruto, was issued with the election certificate.
Before midnight, chaos broke out at Mwakigwena and at the tallying centre after rowdy youth forced their way into the centre chanting Haki Yetu.
They accused the officials of not letting all the ballot boxes in for tallying.
Malindi MP Aisha Jumwa urged the IEBC to announce the results and declare Feisal the winner, saying it was a competition and Boga's team should concede.
The by-election in Msambweni and Kwale County puts to test the political might of tanga tanga against kieleweke in the coming 2022 elections.