The move is part of a wider deal with parent company Orbitz Worldwide, which will provide similar functionality on the main MSN portal in the US.
It replaces an existing deal with Expedia to provide search and booking facilities on the MSN Travel channel.
Tools on MSN.co.uk/travel will include hotels, flights and car hire via the Ebookers engine as well include existing travel-related editorial content and forums.
Microsoft’s recent purchase, Farecast, is expected to be added into the MSN platform in the future.
Orbitz chief executive and president Steve Barnhart said: “Our partnership with MSN will provide additional visibility and traffic to both Orbitz.com and ebookers.com, strengthening growth in both the United States and the UK.
“As one of the largest Internet destinations in the world, MSN represents another significant win for growing our co-branded distribution.”