The Bord Pleanala decision has been welcomed by the Dublin Docklands Development Authority (DDDA) and many local politicians.
The DDDA is responsible for regenerating the docklands area and had criticised many aspects of the Spencer Dock scheme at the board's oral hearing last March.
Its chief executive, Mr Peter Coyne, said the authority remained committed to the "full development of the national conference centre and the entire site as quickly as possible" and in accordance with the authority's master plan objectives for the docklands area.
The Green Party councillor, Mr Ciaran Cuffe, expressed delight with the ruling which, he said, was good for Dublin, as well as for community and conservation groups. Mr Cuffe was one of eight appellants who opposed parts or all of the scheme at the Bord Pleanala oral hearing in Dublin earlier this year.
The appeal was against a decision by Dublin Corporation to grant partial planning permission for the development.
Mr Cuffe said he hoped CIE, which is part of the consortium behind the Spencer Dock proposal, would consider selling its portion of the site to the DDDA for it to develop. CIE owns most of the 51-acre site, which accounts for a quarter of all land capable of development in the docklands.
A Fine Gael councillor, Mr Gerry Breen, who had also appealed the corporation's decision, said the board's ruling was "a victory for common sense and a victory for our capital city."
Labour Party Senator Joe Costello said the planning application should not have been submitted until Dublin Corporation's urban height and density study was completed.
"The decision by An Bord Pleanala further underlines the need for proper and comprehensive planning before any major urban developments are given the go-ahead," he added.
Another appellant was the multi-millionaire financier, Mr Dermot Desmond, who was involved in the nearby International Financial Services Centre. A representative of Mr Desmond said he was not available for comment last night.
However, Mr Paul Keogh, an architect who acted on Mr Desmond's behalf at the oral hearing, described the decision as "a victory for planning and urban design, as opposed to the purely quantitative decision which the corporation made".
He said he presumed the developers would now pay more attention to the DDDA's master plan.
An Taisce said it welcomed the board's decision overall, but regretted that it had sanctioned the demolition of a listed building, Campion's Pub.