Kensington Palace said Ms Ptak, owner of the Violet Bakery in Hackney, will create a cake incorporating 'the bright flavours of spring' for the May 19 wedding. It will be covered with buttercream and decorated with fresh flowers.
It is believed to be the first time a Royal couple have eschewed tradition by not serving a fruit cake to their wedding guests.
The Duke and Duchess of Cambridge chose Fiona Cairns to make their 2011 wedding cake, a traditional multi-layered fruit cake with a floral design.
American former actress Ms Markle, who used to run her own lifestyle website The Tig, previously interviewed Ms Ptak for her blog.
In a statement, Ms Ptak said: 'I can’t tell you how delighted I am to be chosen to make Prince Harry and Ms Markle’s wedding cake. Knowing that they really share the same values as I do about food provenance, sustainability, seasonality and most importantly flavour, makes this the most exciting event to be a part of.'
Ms Ptak formerly worked as a pastry chef for Alice Waters at Chez Panisse in Berkeley, California.
She started her own business as a stall in Broadway Market, east London, cooking from home, before opening her organic bakery.
Kensington Palace said Harry and Ms Markle 'are very much looking forward to sharing this cake with their wedding guests'.
Ms Ptak, who was raised in California, focuses on using seasonal and organic ingredients in her cakes. After the announcement on Tuesday, she told of her excitement on Instagram, saying she and the Royals 'share so many of the same values regarding food provenance, sustainability, seasonality and of course, flavour!'
Violet Bakery, in Wilton Way, is described on its website as serving cakes that are 'baked with organic flour, sugar, milk and eggs.'
It adds: 'Many of the other ingredients are organic as well, like our Madagascan vanilla pods and pure cane molasses.
'Limited edition buttercream icings that adorn our birthday cakes, cupcakes, and fill whoopie pies and biscuits, change with the seasons.'
Tatler, the high society magazine, described Violet as an 'East London hotspot' that 'serves the best American-style bakes around'.
It added: 'The rustic café feels a bit like stepping into your cool auntie's kitchen. We could quite happily waste away an entire Sunday afternoon here.'