National Assembly Speaker Justin Muturi has upheld the vote for the eight percent levy on petroleum products.
President Uhuru Kenyatta made the proposal after widespread opposition to a 16 percent Value Added Tax (VAT).
Mr Muturi's decision came shortly after he ordered a second round of voting, an announcement which sparked persistent protests by Members of Parliament.
The MPs shouted demands for a zero percent rate, some telling reporters at Parliament that they were obligated to fight for their people.
The second vote was ordered after the number of MPs in the House during the first vote was disputed.
Speaker Muturi said the screens showed that there were 352 MPs, more than the 349 members.
Speaking later ahead of a planned second vote, he said there were 215 members but his reiteration of what the orders state were met with shouts that forced him to suspend the special sitting for 15 minutes.
He suspended the session for the Information, Communication and Technology department to rectify the anomaly.
The outcome of the first vote was upheld after the Hansard entry was confirmed as valid so there was no second vote.
The protests persisted even as Mr Muturi announced an adjournment until October 2 at 2.30pm.
In an address to journalists, several legislators accused Mr Muturi of failing to exercise patriotism and termed the vote a sign of "darks days for legislation".
The Speaker and Majority Leader Aden Duale were described as a "shame" and the public urged to rise to keep Kenya from going in the wrong direction.
Mr Duale, the Garissa Town MP, said: "No legislators were sent to perform their duties at Parliament through clapping and singing. Mapambano (the struggle) is on the floor of the House."
The Jubilee Party member told reporters that his duty is to employ "a number of tricks" for the government agenda to be complied with. He said that part of his business was to ensure the threshold was not reached.
"The Hansard saved me. It is very clear ... the required number of 233 must be present before a vote is taken," Mr Duale said. "The count showed there were 215 of us. Since we could not reach the threshold, the item was lost so we moved on. When they realised they did not have the numbers, they displayed all manner of behaviours."
The Majority Leader apologised on behalf of the members for the shouting matches and said his hope is that the President will sign the Finance Bill into law.
Regarding impeachment, he noted that the Majority Leader cannot be impeached but that a decision can be made for his removal. This he pointed out however, is a move that can only be made by his party.