One person was arrested and Tesco said the damage was “minimal”.
A Sainsbury’s spokesperson said the decision to move kosher items was not politically motivated and had been an “isolated decision in a very challenging situation”.
The company is not expected to investigate further or take action against the branch manager.
In recent weeks a number of Sainsbury’s stores have been forced to close temporarily due to anti-Israel protests.
Shopper Colin Appleby, who witnessed the incident in Holborn, wrote on Facebook: “This is their kosher section. It contained produce made in the UK, Poland and Israel.
“When I asked a members of staff what had happened they replied ‘We support a Free Gaza’.”
Dozens of customers criticised the company’s decision on Facebook, saying they would boycott stores.
Sainsbury’s repeated its statement that the removal was for security reasons.