Sussex Police are investigating the incident which took place at a Sainsbury's store on Old Shoreham Road in West Hove shortly after the vicar had exchanged the cash into dollars.
Rev Lynda Hulcoop, a minister at Southwick Christian Community Church, had exchanged the money on 23rd January ahead of a mission trip to Zimbabwe.
The minister and her congregation had raised the money to support a maize-growing project and a special needs school.
After picking up the money from the bureau de change, two young women followed her to the exit and swiped the bundle of bank noted from her bag.
Rev Hulcoop said: "Normally our charity sends money by bank transfer but this option is no longer viable as the banks only allow people to withdraw US$100 per day involving many long hours of queuing. Thus we had to take cash."
The minister went ahead with the mission trip and said the fact she could not bring the lost money with her was a real injustice.
"Greedy people preying on others for their own gain have stolen money meant for children and families in desperate need in a country on the verge of collapse. The whole community who gave so generously feels the offence very keenly."
Sussex Police are still searching for the suspects identified in CCTV footage.