A man and woman "believe to be linked to Palestine Action" were arrested on St Clare Street following the incident on Wednesday, City of London Police has confirmed.
"They allegedly sprayed paint on a building and caused damage to the glass," said the force on X, formerly Twitter.
"They have been bailed with conditions, pending further investigations."
Palestine Action said on X on Wednesday it had targeted Swiss global transport and logistics company Kuehne+Nagel, which has offices at the St Clare Street premises in Aldgate.
A photo showed red paint splattered across the front of the building.
Palestine Action accused the company of providing insurance for a firm that transports Israeli weapons used in Gaza.
It said on its website it had left the London office "drenched in paint".
It said it also targeted another Kuehne+Nagel premises in Milton Keynes, where activists "sprayed the entire front of the building in blood-red paint and shattered windows".
Kuehne+Nagel has been approached by the Standard for a comment.