The Liberal Democrat leader on the city council won 21 votes during today’s full council meeting, beating Cllr Jones - the council’s Conservative party leader - by one vote.
Cllr Jones first took on the role of city council leader in 2014, replacing Cllr Vernon Jackson.
It comes after no party won a majority on Portsmouth City Council in the local elections earlier this month.
The Conservatives will remain the largest party on the councils but do not have overall control.
Cllr Vernon-Jackson has served on the city council since 2003.