BECTU, the NUJ and Unite said that the BBC's offer of a 1% pay increase for 2012-2013 (subject to a minimum increase of £400) remains "derisory", but they have "secured concessions on conditions which will provide valuable protections during the current licence fee period".
BBC bosses and the unions finally reached agreement in talks yesterday, after staff were balloted on potential industrial action during the Jubilee next month.
The BBC has stuck by its guns with the 2012/13 pay offer, despite unions saying that it is below inflation, but it has also offered commitments aimed at ensuring a similar dispute is avoided in future.
The agreement says: "Whilst it is accepted that, as in many organisations, cuts in funding will have an impact on staff, it is believed by both the joint unions and management that a continuous pattern of annual settlements which represent a real cut in pay are neither desirable nor sustainable.
"A great deal is expected from people in the BBC and whilst no-one is immune from the impact of the reduced funding, employees must be paid fairly."
Alongside the dispute over pay, staff were also said to be upset over plans to cut allowances for unpredictable working, while there was "dissatisfaction" with the staff appraisal system and "dismay at the BBC's failure to implement an agreement reached last October on staff redeployment".
Around 2,000 jobs are under threat under the BBC's Delivering Quality First initiative announced last October, as the BBC seeks to save around £670m by 2016/17.
The unions said that they have secured agreement that BBC managers must review a central database of all staff at risk of redundancy before advertising any new vacancies either internally or externally.
"We are now making constructive and positive progress with trying to find proper and long term solutions," said Michelle Stanistreet, the NUJ general secretary.
"The immediate risk of redundancies at TV Current Affairs and the World Service has been averted. This has only been achieved because NUJ members have stood solidly together in opposition to compulsory redundancies.
"We have been deeply concerned by the failure of the redeployment process so the settlement today addresses the problem which we welcome.
"The BBC's stance on pay is disappointing, but the package of concessions on other pay-related issues and appraisals addresses key concerns for journalists across the BBC."
BECTU general secretary Gerry Morrissey added: "There is absolutely no question that the BBC's handling of this year's pay talks will continue to anger staff and what is more, our members, not least in London, will suffer financially.
"However from the soundings we have taken, viewed nationally, pay was not the primary concern and in light of this we doubted the success of strike action over the Jubilee weekend."