The new agreement also kept the provision of five weeks' annual leave for all existing staff and increased the base hourly rate for drivers with at least six months' experience to $24 per hour.
204 drivers voted to reject the payout.
They also passed a vote of no confidence against NZ Bus management, and will be looking into the possibility of a multi-employer agreement with other bus operators.
Council of Trade Unions President Richard Wagstaff says the work conditions that NZ Bus wants to cut were fought for tooth and nail.
Union Secretary Kevin O'Sullivan said he was not surprised by the rejection of the offer following the "bullying tactics" of NZ Bus.
Bus drivers vote on NZ Bus's new pay offer today. Photo / Kasharn Rao
"Members don't want to give up their rates and allowances - these are the parts of the agreement that give them some control over their work lives and their health and safety," he said.
"The company has tried bullying tactics with its so-called indefinite lockout and now it has tried the bribe of a big one-off payment.
"Neither has worked because our members know how important their conditions are to their long-term take-home pay and to their ability to manage their work lives.
He said the union was giving NZ Bus and its owner Next Capital until May 27 to negotiate a fair deal before they resumed strike action.
Bus drivers meet to vote on important pay offer. Photo / Kasharn Rao
NZ Bus chief operating officer Jay Zmijewski said the company was "very disappointed" with the union's decision.
"We maintain our strong desire to see pay rises and incentives paid to our drivers and their families and cannot understand how such a generous offer was dismissed out of hand despite the extensive mediation and negotiation process that has been undertaken."
Zmijewski said the company has spent considerable time listening to the union's concerns and participated in an extensive mediation process in good faith.
He said significant improvements were made to the original offer to take account of concerns raised by the union and they awaited its next steps
A number of bus services were cancelled while the meeting was held between 9am and 3pm.
The affected bus routes were: 2, 3, 12, 14, 18e, 20, 21, 22, 30x, 31x, 81, 83, 84.
Last month NZ Bus issued a lockout notice to drivers who walked off the job for a 24-hour strike following a breakdown in their Collective Agreement negotiations.
However, the Employment Court ruled the lockout unlawful, bringing it to an end.
Council of Trade Unions president Richard Wagstaff came out in support of Wellington bus drivers today.
"NZ Bus have shown themselves to be out of touch with the needs of running a proper public transport system. It can't be done while trying to strip it for profit. Drivers themselves have shown they want no part of that strategy. "
