Sabre Travel Network travel agents in Germany, Switzerland and Austria have been exempted from fees Lufthansa plans to impose in the summer under its Preferred Fares scheme.
The exemption came after the GDS, the third largest in Germany, signed a deal with the national carrier and its subsidiary SWISS.
Under the agreement, all Sabre agents in the three countries which sign up to Lufthansa's programme will have access to all the two carriers' fares and inventory without paying the stipulated fee.
Under the Lufthansa/SWISS proposals, fares will go up by 15 one way and 30 for a round trip on tickets bought in Germany and Austria from July 1.
Prices for tickets bought in Switzerland and Liechtenstein will go up from October 1.
But the carriers said they would continue to make available the current lower fares after those dates.
These will be called "preferred fares" and will be subject to the surcharge if booked through a GDS.
Lufthansa will charge agencies 4.90 plus VAT per coupon and SWISS will charge CHF8 (5) per booking. It is this fee from which Sabre agents will now be exempt.
If the preferred fares are booked through the two carriers' travel agent portals, or direct from the airlines' websites, call centres or ticket counters, there will also be no fee.
The scheme, announced in January, has angered agents in all three countries who have claimed it is Lufthansa's method of cutting 2.5m from its distribution costs.
There have also been calls to boycott the programme.
The Sabre-Lufthansa deal comes as agents' representatives are meeting officials from the Bundeskartellamt - the German monopolies' authority - in Bonn today (May 9).
Martin Cowley, Sabre's senior vp in the EMEA, said: "This is fantastic news for our agency customers who have told us they want to continue booking via the GDS because it's the most efficient and productive way of working.
"It's our standing philosophy to find solutions that meet the needs of everyone in the industry and today's announcement with Lufthansa and SWISS reinforces our ability to deliver this while highlighting the continued value of the GDS.
“We're confident today's announcement will be well received by the industry, delivering benefits to our existing agents and new customers we hope to attract as part of our continued expansion in Europe."
Thierry Antinori, Lufthansa's executive vp for marketing and sales, said: "Sabre is an important distribution channel and an efficient marketplace for all Lufthansa fares.
"Thanks to the extension of our agreement, we can now offer our Preferred Fares without any additional fees to participating travel agencies using Sabre."
Harry Hohmeister, SWISS chief network and distribution officer said: "Sabre is a key partner in our distribution structure.
"Our extended agreement with Sabre will sharpen SWISS's competitive edge and provide all the travel agencies that use Sabre with access to all SWISS and Lufthansa fares without additional fees."