He has "decided to leave the business to pursue opportunities outside of the company", the company said.
Jacob oversaw the unification of all Publicis Groupe’s media agenices in a new operating unit, Publicis Media, at the start of 2016 as part of a group-wide restructuring.
He was previously the chief executive of Starcom Mediavest Group EMEA, Australia and Canada during a 15-year spell at Publicis Groupe.
Publicis Media said it grew under Jacob’s leadership as it retained and expanded Procter & Gamble’s account in the biggest UK media review of last year and picked up international business for Fiat Chrysler owner FCA Group and Visa.
Publicis Media said it will announce new EMEA leadership imminently.
Jacob said he felt it was "the perfect time for my next challenge".
He went on: "I have been given great opportunities within Publicis since joining in 2003 and have thoroughly enjoyed helping build a strong and growing media business in EMEA."
Publicis Groupe has adopted a strategy dubbed the Power of One in which it is bringing together staff from agencies across the group for clients including P&G.
The group also appears to be shifting some responsibilities from pan-regional leaders to country managers such as Annette King, who was head-hunted to be the first UK chief executive of Publicis Groupe, and Agathe Bousquet, who was named president of Publicis Groupe in France last year.
Steve King, global chief executive of Publicis Media, said: "Iain has done a terrific job of launching and building Publicis Media in EMEA over the past two years."
Publicis Groupe reported organic revenue growth of 1.3% in Europe and 3.1% in the Middle East and Africa in 2017.
The group announces first-quarter results on 19 April.