Two prints, worth a combined £33,000, were taken after a suspect stormed the Exhibitionist Gallery in Blenheim Crescent, Notting Hill, London, between 3am and 3.30am on Monday.
Metropolitan Police said a suspect entered the gallery by forcing the front doors and drove the items away in a dark-coloured hatchback-type vehicle towards Ladbroke Grove.
The stolen pieces feature multi-coloured dots and are signed by the artist.
Gallery manager Nathan Engelbrecht, 31, said he suspected the thieves would have known the value of the prints, which he had only acquired four days earlier and planned to unveil to clients on Tuesday.
"The speed at which it happened - we got them on Thursday and they're gone on Monday - just seems a bit coincidental," he said.
"It seems like it was targeted. It's a bit disappointing - as soon as you get a big name in the gallery, it just gets ripped off."
Mr Engelbrecht said those responsible did not go for anything else in the gallery.
The larger of the two stolen works is entitled Pyronin Y and is 40in by 46in. It was created in 2005 and is worth £15,000, police said. The second work is entitled Oleoylsarcosine and is 26in x 35in. It was created in 2008 and is worth £18,000.
Hirst was awarded the Turner Prize in 1995.