Two officers were in Chapter Street, in Westminster, at about 3.42pm on Sunday when they spotted the suspects, who were armed with knives.
The shopkeeper had forced the men out of the store and, as the officers challenged the men, the woman officer was stabbed in the abdomen before chasing the pair along Vauxhall Bridge Road.
The suspects were arrested shortly afterwards with the help of firearms officers, while the injured officer was taken to hospital with an injury that is not thought to be life-threatening.
Chief Inspector Simon Brooker, Central West BCU, said: "This shows precisely the kind of danger officers face every single day as they work to keep the public safe.
"For this officer to be stabbed on duty is unacceptable but, fortunately, she does not appear to be seriously injured.
"I applaud her bravery in responding to this call. This courage is typical of Met officers as they go about their duties."
Mayor of London Sadiq Khan said: "My thoughts and prayers are with this brave police officer who is receiving treatment in hospital after she was stabbed while on duty, intervening in a robbery, this afternoon.
"Every day our courageous police officers put themselves in harm's way to keep Londoners safe.
"I am sure all Londoners will join me in wishing her a speedy recovery.
"Attacks on our police are utterly unacceptable and perpetrators will feel the full force of the law."