Don Robinson, founder of the Winston Churchill's Britain at War Experience in London, has offered a £500 reward to catch the culprits.
He has also donated a further £600 to the British Legion to make up for the theft.
A spokesman for the Royal
British Legion said: "It's such a shame. I am sure Sir Winston Churchill would be turning in his grave."
The two men distracted staff at the museum and managed to prize free the charity box, which was nailed down.
Mr Robinson, who opened the museum back in 1992, said: "I felt disgusted when I heard about it. You wonder what the world is coming to when people do things like that."
It later came to light the thieves had also stolen a poppy collection from the nearby HMS Belfast museum.
"To steal from one place is bad enough, but to do the same thing somewhere else is just appalling," added Mr Robinson.
Museum cashier Tracy Gordon said she thought the pair were drunks.
Southwark Police are investigating the incident.
Last month, Scarborough residents were outraged when thieves stole a walking stick from an elderly ex-serviceman as he was standing in the cold selling poppies.
Jim Carson, 76, brother of Irish comedian Frank Carson, had propped his wooden stick against the wall of the Next shop on the corner of Westborough and York Place while collecting for the Royal British Legion appeal.
With his stick gone, Mr Carson was forced to limp back home to Filey Road. But a member of the public found it in a public telephone box in St Nicholas Street several days later.