Cook will transfer around 3,000 hotel contracts from across the group to Sunhotels - Webjet’s European online accommodation business.
The agreement builds on a partnership Sunhotels already has with Thomas Cook in its Nordic markets.
The contracts will be added to Sunhotels’ existing inventory of 75,000 hotels worldwide, which will also be offered to Thomas Cook.
Thomas Cook said the partnership will allow it to focus on growing its “core differentiated holiday offering” while “providing customers with a wider range and choice of complementary hotels in a more efficient way”.
Sunhotels will also take responsibility for managing an updated health and safety audit process.
Cook said the move represents an “important step forward” in its group-wide transformation programme, known as the New Operating Model.
The business said that by moving the direct contracting for complementary hotels to a “trusted partner”, it will be able to simplify its IT platforms and business processes across its 15 source markets.
Thomas Cook chief executive, Peter Fankhauser, said: "Entering this new relationship with Webjet will transform the way in which Thomas Cook offers a wide choice of hotels to customers.
“It provides us with a low-cost production platform for our complementary offer across all our source markets, enabling us to streamline our systems and processes while at the same time ensuring greater certainty over the quality of hotels that we offer our customers.
“This frees us up to focus on growing our differentiated holiday offering, the area where we know Thomas Cook can really make a difference."