After a postal ballot, 61.4% of of the union's members employed at the BBC voted in favour of the package, which was tabled by management last month after intervention from BBC director-general Mark Thompson.
The dispute focused on the 2006 2.6% pay offer to BBC employees, 0.7% below the current 3.3% RPI inflation rate. This offer was deemed unacceptable by Bectu, the National Union of Journalists and Amicus.
Members at BBC Worldwide accepted the deal with 89.7% in favour, while 82.7% of those working for BBC Resources, voting only on the pension changes, accepted.
A parallel ballot of the NUJ's journalist members produced an opposite result, with 59.4% voting to reject the pay and pensions offer.
Neither union made any recommendation on which way members were advised to vote -- a condition imposed by the BBC when it tabled the compromise package.
Bectu said that its membership had accepted the increase and the changes to pensions, which will particularly affect new staff from September this year, but that it had plans to "warn the BBC that the modest majority in favour of the package demonstrates deep unhappiness among staff".
The union added: "Many members remain angry at the below-inflation pay offer in a year when top BBC executives were given bumper increases."
The BBC's top 10 executives were collectively paid a total of £232,000 in bonuses, according to last month's BBC annual report.
Representatives from Bectu, the NUJ, and technicians' union Amicus plan to meet on September 1 to discuss their joint response to the BBC.
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