The newly found programmes - which introduce the character of Alistair Lethbridge-Stewart, better known to audiences as The Brigadier - will be available on iTunes from today and will later come out on DVD.
Phillip Morris, the director of Television International Enterprises Archive, unearthed the programmes by looking up the records of overseas shipments of tapes made by the BBC.
The stories, The Enemy Of The World (1967) and The Web Of Fear (1968) and both starring Patrick Troughton as the second Doctor, have now been remastered by BBC Worldwide, the corporation's commercial arm.
More top news
More people are struggling to get through to their GP on the phone, new research has revealed.
A legendary Bunny, leisure centres and protests from the Anti-Nazi League. There's plenty to learn as Murray and Co bid for tennis glory.
Natasha Kaplinsky has interviewed survivors and liberators of Nazi concentration camps to hear untold stories of the Holocaust