Members of Unite union have voted to accept Fujitsu's proposals tabled by mediation service Advisory, Conciliation and Arbitration Service (ACAS).
A four to one majority voted to accept the proposals, in a 72 percent turnout.
The agreement ends the four-month dispute, which saw 10 days of strike action, a lobby of parliament and prolonged uncertainty over redundancies. All related industrial action has now been called off.
Peter Skyte, Unite national officer for the IT sector, said: "Whilst the ACAS brokered proposals do not fully satisfy our members' aspirations, there have been significant changes in the company's position on jobs, pay and pensions over the course of the dispute.
"Unite will continue to work with Fujitsu to avoid compulsory redundancies and press the company for a fairer and more open and transparent pay system that more adequately recognises and rewards the Fujitsu workforce for its contribution to the company's success and for improved pension provision."
Unite started its campaign against Fujitsu following the IT services company's proposal to make 1,200 redundancies in the UK, a pay freeze last year and a plan to close the main final salary pension scheme to future accrual.
Fujitsu then dropped its redundancy targets during the dispute to a planned 834 redundancies, 586 of which were voluntary. During the ACAS talks last week, Fujitsu had lowered the number of compulsory redundancies to 23, from the 42 planned just before the talks began.
Unite has agreed to proposals that mean that remaining employees facing the compulsory redundancies have had an extension of employment until at least 26 March.
In terms of pensions, the consultation period has been extended from October 2009 until at least next Friday (5 March).
In addition to this, a 5 percent increase in pay has been offered as compensation for the change to a defined contribution (DC) scheme, and the final salary pension scheme has been extended to March 2011 at the earliest.
Unite has also obtained a commitment from Fujitsu to make the DC pension scheme contractual for both new and existing members.
Meanwhile, Fujitsu has committed to make pay and benefit scales discussions more transparent and agreed to introduce a minimum basic salary of £12,000, which comes into effect from 1 March 2010. This will be reviewed annually starting on 1 April 2010.
Unite is hoping to achieve minimum earnings of £13,500 at the firm.
In a statement, Fujitsu said: "We are very pleased that the Unite members in Fujitsu have voted to accept the proposals tabled through ACAS by a majority of 81%. This means that all industrial action is now called off which is good news for all concerned."
Unite's strike campaign targeted work on a number of high profile contracts, including with Marks & Spencer, Vodafone, the Home Office, HM Revenue & Customs, the Financial Services Authority, and the Post Office.
The union has also posed questions over whether Fujitsu was discriminating against women and staff from ethnic minority backgrounds in its choice of those targeted for redundancy. Fujitsu strongly rejects any question of discrimination and said it always acted in the interests of equal opportunities.