The move to double the fuel tax to 16% will generate the government an extra 61 billion shillings ($434.94 million) by itself, Kuria Kimani, the chairman of parliament's finance panel, said on Citizen Television.
During a session that ran late into the night, lawmakers from Ruto's ruling coalition defeated opposition attempts to strike out the fuel tax hike as well as a new 1.5% housing tax on employees that will be matched by employers.
They also approved a new withholding tax for digital content creators.
The opposition says the housing levy will strain already squeezed incomes and raise business costs at a time when Kenyans are struggling with high prices for basic commodities.
Ruto's government argues the higher taxes are necessary to stabilize government finances, which have been strained by growing debt repayments and lower than expected growth in tax collection.
The bill now moves to the president for signing.
However, the opposition has threatened to call fresh protests if Ruto signs the tax increases into law. Street demonstrations earlier this year against the high cost of living repeatedly turned violent in the capital Nairobi and elsewhere.
An opposition senator has challenged the finance bill in court, arguing that some of the measures are unconstitutional. It was not immediately clear when the court will issue a ruling.