The Omnicom agency pitched against Havas' Media Planning Group, WPP's MindShare, Aegis' Vizeum and Interpublic's Universal McCann.
Waitrose ended its six-year contract with Brand Connection earlier this year. The Interpublic agency did not re-pitch - the review is thought to have been prompted by its merger with sister agency Initiative, which handles the conflicting Tesco account.
Manning Gottlieb OMD account director Chris Ware will head the Waitrose account team. The win follows a two-month process, handled by Billetts, and a creative review 18 months ago, in which Miles Calcraft Briginshaw Duffy triumphed.
Christian Cull, Waitrose marketing director, said: "Manning Gottlieb OMD showed a deep understanding of the needs of the business and the Waitrose marketing strategy.
"It presented a media strategy heavily geared to delivering on our business objectives. We felt that the agency offered a good team-fit and are looking forward to working together."
Waitrose is currently airing two new TV ads, the first building on the "Who are they?" campaign around the supermarket's Partnership card.
The second, an interactive ad, focuses on the Waitrose Foundation, a partnership created to benefit the labourers who farm the supermarket's South African citrus fruit.
This follows Waitrose's interactive TV campaign for its Perfectly Balanced range, in which viewers could ask a nutritionist questions and win a free box of cereal bars.
Separately, the John Lewis Partnership, which owns Waitrose, is reviewing its £13m creative account, held by full service agency Burkitt DDB. The agency also handles the group's media planning and buying, which will be reviewed if the creative account changes hands.
The John Lewis Partnership is not looking to consolidate Waitrose planning and buying with the rest of its media work. The group is one of the UK's top 10 retail businesses, with 27 John Lewis department stores and 179 Waitrose supermarkets together turning over more than £5bn a year.