Saturday shopping came to a halt in Moreton Hall Sainsburys when water started pouring through the roof over the tills.
The supermarket had to close at about 3pm on Saturday and did not reopen until 9.30am on Sunday.
A Sainsburys spokeswoman said: “We had to close for customer safety. Even if none of the electrical items were compromised, there was the risk of someone falling over because so much water was coming in.”
She said the water had come in through a joint in the roof near the checkout area.
Bury St Edmunds weather recorder Alan Messem, who lives about a mile from Sainsburys as the storm cloud flies, said he measured about 11mm of rain falling in about an hour on Saturday. The meteorological definition of a heavy shower is above 10mm an hour.
But he stressed: “This sort of weather is very localised. It could have been much heavier just a short distance away.”