As part of the recommendation, the deal will no longer be conditional on receiving shareholder approval for the controversial retention payments to be made to Xstrata executives.
If shareholders reject the incentive schemes, the merger will still be able to proceed.
Under the scheme, shareholders will vote on two new resolutions at the court meeting.
"We have decided to de-couple the resolutions to approve the merger from the resolution to approve the revised management incentive arrangements," Xstrata non-executive chairman John Bond said.
"This will, we believe, enable shareholders to vote in line with their convictions in respect of retention arrangements, without influencing their voting intention on the new scheme."
Glencore previously said it was "content" for up to 70 Xstrata managers to receive the payments, worth as much as £173 million ($A269.5 million), but it was known to have been a sticking point with some shareholders.
All other aspects of the deal remain the same, including the ratio of 3.05 Glencore shares for every Xstrata share held, as well as the departure of Xstrata chief executive Mick Davis after six months at the helm of the enlarged company.
"My objective during my time as CEO of the combined group will be to preserve and enhance the value Xstrata's management team has created over the past 10 years through a well-planned integration process, and to lay down the foundations for the combined group's success over many decades to come," he said.
However, Davis will no longer receive retention payments and will be paid only his current contractual entitlement, amounting to about $A15 million.
In an attempt to win over shareholders unhappy about Davis' departure, an operational executive will be appointed and Glencore CEO Ivan Glasenberg, who will take over as CEO when Davis leaves, said he would support the governance structure of the company for at least two years.
"We have always been in favour of the proposed retention arrangements to incentivise key Xstrata employees," he said.
"Their commitment is vital as we look to capture the full synergy and value creation benefits of the transaction, and realise the potential of both companies' strong long-term organic growth plans."
It is expected that the new scheme will become effective before December 31 this year.
London-based Fairfax analyst Carole Ferguson said the deal was likely to succeed.
"The operational executive being proposed by both sides is a way of mitigating the gap left by Mick Davis, although interestingly, the executives on that team will need to be nominated by Ivan Glasenberg, then approved by the chairman and senior non-executive director," she said.
"Given the weak backdrop for the sector, we expect the merger to go through."