The man entered McAuliffe Jewellers in King Edward St about 5.40pm, a police spokesman said.
The offender stole cash and ran away.
No-one was injured.
Several police officers were deployed to the store and talked to owner Robert McAuliffe.
Mr McAuliffe did not return calls from the Otago Daily Times last night.
The shop had been targeted by thieves twice in the past eight months.
Burglars stole thousands of dollars of jewellery from the 60-year-old family store in an early morning raid in November last year.
Offenders used a ladder to smash part of the wall to enter the building and broke into a cabinet before leaving with the goods via the ladder.
Anyone who witnessed anything suspicious near McAuliffe Jewellers or in King Edward St yesterday is urged to contact police.
Dunedin police (03) 471-4800, Crimestoppers 0800 555-111.
