The Senate voted 29-9 today to dismiss Governor Deval Patrick’s attempts to further increase the gas tax to help fund the state’s $800 million transportation finance bill. The amendment will now go back to Patrick’s desk.

Patrick has promised to veto the legislation if his changes were not included, but Senate President Therese Murray said after the vote Thursday she is confident the Senate will have the votes to override a veto.

“We put forth what I believe is a very good bill that addresses the needs of the Commonwealth far into the future,” Murray said.

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The bill, first introduced in the State House in April, is meant to provide relief to the state’s beleaguered transportation system, close the budget deficit at the Massachusetts Bay Transportation Authority, and fund a few modest new projects.

The legislation will raise the gas tax by three cents, pegging it to inflation, add a $1 tax to tobacco products, and place a further tax on computer software services. The legislation also relies on redistribution of money from an underground storage tank cleanup fund.

The sticking point between Patrick and legislators centers on a disagreement over the reliability of future toll revenue: After 2017, the existence of tolls on the Massachusetts Turnpike is no longer legally mandated. If the tolls come down, the state’s Department of Transportation could end up with significantly less than the promised $800 million.

Patrick says that’s a significant risk, and has argued for a further increase in the gas tax to accommodate for any potential lost toll revenue. But Murray said Patrick is not giving enough credit to legislators who should be trusted not to leave the state’s transportation department out to dry in coming years.

“If in 2017 there’s a need, there’s a legislature that will be here,” Murray said. “This is a very good bill. I hope that in the end he’ll take credit for that.”

Patrick said he met with senators Thursday morning to discuss his proposed changes. He vowed to veto the bill on principle, even though the Senate likely has the necessary two-thirds vote for an override.

Still, the governor said, he understands that the bill was significant progress for the state.

“We’re talking about the difference between 630 million and 800 million dollars in new transportation investment: that’s not zero,” Patrick said. “It’s not like we have nothing to show for nearly a year’s work.”

But even members of the Senate who voted against Patrick’s changes acknowledged that the toll issue is cause for some concern. Senator Benjamin B. Downing, a Democrat of Pittsfield, said he worried that the uncertainty shrouding the future of tolls post-2017 will affect the state’s ability to borrow money for transportation investment projects such as the aging Interstate-91 Springfield viaduct or the Green Line extension.

“In the absence of certainty on those tolls, there will be an impact on capital projects in the future,” Downing said. “We will have to revisit this issue.”

Transportation Secretary Richard A. Davey said those concerns are real: Even if tolls are not eliminated in the future, he said, bond agencies are not in the habit of banking on the political whims of the legislature years down the road. And without bonds, many projects the state wants to pursue will have to go on the back-burner, he said.

“We can’t say to investors, ‘Trust us, the money will be there to pay you,’” Davey said.