The man was off work this week as he was not ready to return to the store after his ordeal. He was not injured.
After the men left the store, he emerged from the chiller and called police.
Detective Constable Joseph Niupopo said the men took the entire cash drawer, cigarettes and bottles of alcohol. They then ran out of the shop, got into a waiting vehicle and drove off.
The manager believed about $1000 was taken.
Almost 24 hours later robbers burst into Mt Eden Wines and Spirits on Mt Eden Rd, 3.2km away.
Mr Niupopo said the men were heavily disguised when they went into the store at 9.20pm.
The store is blocks away from Eden Park, where the Rugby World Cup semifinal between the All Blacks and Australia had just begun.
"Again, one male armed with a black pistol presented it at the two staff members while another male took cash, cigarettes and alcohol," he said.
"A staff member suffered moderate injury during an altercation with one of the offenders."
The manager, who spoke to the Herald on the condition his name was not published, said the employee had to go to hospital with a head injury.
"He needed stitches, there was a lot of blood."
The men fled the store and got into a stolen white Honda Civic, which was later found dumped on a nearby street.
Mr Niupopo said the man brandishing the pistol in the second robbery was about 182cm in height, skinny and wearing a black balaclava, jacket and pants. The other man was dressed in black and wore white gloves.
He wanted to speak to anyone who recognised the men or had information about the robberies.
* Anyone with information can contact Detective Constable Niupopo on (09) 820-5630.