The Newspaper Guild rejected the package, which included a 23% pay cut, by a vote of 277 to 265. The union has 670 members, meaning that 128 did not take part in the crucial vote.
Despite the no vote the New York Times Company has said that as the two were now at an impasse the Boston Globe would implement the wage reduction next week.
A spokesman for the Boston Globe, Robert Powers, said: "As we have stated, the $10m in cost savings from this multifaceted proposal is essential to The Boston Globe's financial future.
"We regret having to take this action, but have no financially viable alternative."
The Newspaper Guild said it would fight any attempt to impose pay cuts by filing for unfair labour practice charges with the National Labor Relations Board and federal courts.
Staff will have to now live with a major loss of income as the union attempts to fight the cuts, which are unlikely to be blocked by courts.
Members of the Newspaper Guild have complained that journalists and other union members are suffering and management is not taking its share of the cost cutting at the paper, which is on course to lose $85m (£52.7m) this year.
The Newspaper Guild was the last of the newspaper's six unions, which also include the Teamsters, to vote.
The other five unions had already agreed to cuts amounting totalling $10m, but the New York Times Company was looking for another $10m in cost savings from the Guild, the newspaper's largest union with almost 700 members.
After the vote Newspaper Guild president Daniel Totten said: "With today's vote, members of the Boston Newspaper Guild have said that The New York Times Company must do better than the offer that was presented.
"Globe workers and the New England community understand that the quality of The Boston Globe -- an institution so vital to the life and culture of the region -- depends on the fair treatment of the men and women who work so hard to produce it."
In April the New York Times Company said it would close the Boston Globe if it could not make major cost savings.
It has since pulled back from this stance, but closure or sale remains an option for the loss-making newspaper, which is the largest in New England.
How staff reacted to the vote
Donovan Slack, a reporter at the Boston Globe told the New York Times: "For weeks I’d wake up in the middle of the night with my mind going around in circles, said who said she decided over the weekend to vote for the package. I can't afford to gamble with a quarter of my pay. How can I pay my mortgage?"
Speaking to the Boston Globe, Globe photographer Dina Rudick who voted yes, said: "The industry is in peril, and for us to expect things to remain the same is ludicrous. We may not like it, but we have got to evolve, and evolution may look like shrinking for now."
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