Miles Calcraft Briginshaw Duffy and Farm are now expected to split the high-profile £12 million account.
Kitcatt Nohr Alexander Shaw has been reappointed to handle direct marketing, while Mediaedge:cia has won the media planning and buying duties from PHD.
MCBD and Farm's exact shares of the business will be determined after campaigns developed for the pitch by the two agencies have been put into research.
The DoH kicked off the review of its anti-smoking account in November last year.
Five teams of agencies lined up as the DoH signalled a search for a more integrated approach to its advertising.
MCBD, Mediaedge:cia and Kitcatt Nohr formed one team. The three competed against AMV, Craik Jones Watson Mitchell Voelkel and PHD; DDB London, ZenithOptimedia and Chemistry; and Farm, Naked Communications and Personal. Bartle Bogle Hegarty, Manning Gottlieb OMD and WWAV Rapp Collins also took part, but pulled out in the early stages.
Cilla Snowball, AMV's group chairman, said: "We thank the DoH and COI for the privilege of working on this important campaign over the years and we wish them every success as they move into a new chapter."
In a separate appointment, COI and the Welsh Assembly have appointed Golley Slater to create a new anti-smoking campaign in Wales after a pitch against Chick Smith Trott and BDH/TBWA.
Comment, page 44.