Oxfam described her work for the fizzy drinks company as "incompatible" with her role as an Oxfam global ambassador, stating that it believes SodaStream "furthers the ongoing poverty and denial of rights of Palestinian communities".
Oxfam said it is opposed to "all trade from Israeli settlements which are illegal under international law". The SodaStream factory is in the occupied territory of Maale Adumim.
The 'Avengers Assemble' actress signed a contract to promote SodaStream earlier this month, and will appear in an advert for the company during Sunday's Super Bowl American Football showpiece.
In a statement her publicist said that she "has respectfully decided to end her ambassador role with Oxfam after eight years".
It continued: "She and Oxfam have a fundamental difference of opinion in regards to the boycott, divestment and sanctions movement. She is very proud of her accomplishments and fundraising efforts during her tenure with Oxfam."
The full statement from the charity reads: "Oxfam has accepted Scarlett Johansson’s decision to step down after eight years as a global ambassador and we are grateful for her many contributions.
"While Oxfam respects the independence of our ambassadors, Ms Johansson’s role promoting the company SodaStream is incompatible with her role as an Oxfam Global Ambassador.
"Oxfam believes that businesses, such as SodaStream, that operate in settlements further the ongoing poverty and denial of rights of the Palestinian communities that we work to support. Oxfam is opposed to all trade from Israeli settlements, which are illegal under international law.
"Ms Johansson has worked with Oxfam since 2005 and in 2007 became a Global Ambassador, helping to highlight the impact of natural disasters and raise funds to save lives and fight poverty."
SodaStream will broadcast the full ad in the UK on Monday (3 February) on Channel 4.
The ad has already been in the news after the removal of the final line of the ad due to a mention of soft drinks competitors Coca-Cola and Pepsi, reportedly by Super Bowl broadcaster Fox. The final cut line was "Sorry, Coke and Pepsi".