Ugarte, 25, sustained a knee ligament injury during Uruguay's final World Cup group game against Spain and was taken off on a stretcher, having landed awkwardly in a challenge with Barcelona's Pedri.
The Uruguayan started all three of his country's group matches before their exit and posted on social media afterwards that he had suffered "the most serious injury a footballer can face."
A club statement read: "Manchester United can confirm that Manuel Ugarte has undergone successful surgery to address a knee-ligament injury, which he suffered whilst representing Uruguay at the FIFA World Cup.
"Ugarte will now begin the rehabilitation stage of his recovery and will be carefully managed by the club's medical and performance staff.
"Everyone at Manchester United wishes Manuel well for his recovery and will be supporting him every step of the way."
United have not disclosed the precise ligament affected or given an exact recovery timeframe, though reports suggest a window of six to twelve months, meaning Ugarte is unlikely to feature again until deep into the 2026-27 campaign at the earliest.
Fifa's insurance scheme will help cover part of Ugarte's salary, believed to be around £120,000-a-week, during his absence. The governing body pays out daily from the 29th day of an injury, with United expected to receive approximately £13,500 per day up to a total cap of £5.6m.
Should Ugarte remain sidelined for nine months, United would collect roughly 244 days of compensation, totalling around £3.29m, though the scheme does not cover any missed bonuses.
Manchester United had been looking to move Ugarte on this summer after two difficult seasons following his £50m arrival from Paris Saint-Germain in 2024, having made just 22 Premier League appearances last season, only eight of them starts. Those plans are now on hold, with the club instead expected to bring in further midfield cover following the injury, having already signed Andrey Santos and Youri Tielemans this summer.
Ugarte, who went under the knife on 15 July, later wrote on Instagram: "A few days have passed since everything happened. Hitting rock bottom will make me stronger in every sense, and I truly believe that's the case here."
He thanked both the Uruguayan federation and Manchester United for their support.
United face Wrexham in their first pre-season friendly this weekend as manager Michael Carrick continues to reshape his midfield options.