The Cardiff City manager has led tributes to Emiliano Sala after a body recovered from the wreckage of a plane on the seabed was identified as that of the Argentinian footballer.

Neil Warnock said he believed the confirmation that the 28-year-old had died in the crash would bring peace to the player’s family, who organised their own private search for the missing aircraft.

He said the football club’s thoughts were also with the family of the pilot, David Ibbotson, who remains missing almost three weeks after the crash off Guernsey in the Channel. “They will be going through hell, our thoughts are with David Ibbotson and his family,” Warnock said.

It has emerged that the Premier League club will pay for Sala’s body to be returned to Argentina when it is released by the coroner. Nantes, the French Ligue 1 side that sold Sala to Cardiff, are to retire the No 9 shirt that he wore.

Warnock said he heard on Thursday night that the body recovered from the plane was Sala’s.

Speaking at Cardiff City stadium on Friday, he said: “I got a phone call last night. It was strange. It brings the family peace and offers them comfort.”

Play Video 1:15 Emiliano Sala 'will leave an eternal memory' says emotional Nantes coach – video

Warnock said he understood the family’s desire to organise their own search, which they financed though a crowdfunding campaign: “When I spoke to Romina [Sala’s sister], she couldn’t let it go. I wouldn’t have been able to let it go. To start that up as they did and get such a response is amazing.”

Paying tribute to the striker, Warnock said: “He was a scruffy type of player that for me would score 10 to 15 goals every year at the top level and work hard as a team player – somebody who can do something special, but he was a really nice lad.

“He wasn’t a young kid. He was in his prime and knew he had things to prove. He’d been in a comfort zone in France. He was a little bit fearful of the challenge ahead but I think he knew he had to try to make that step.”

Warnock also praised the way football fans had responded to the tragedy. “When something like this happens it brings all the football family together. I think it shows that everybody is thinking on the same wave length.”

He said he had made a night-time visit, when nobody else was around, to the shrine of football shirts, scarves and flowers outside the stadium.

Warnock said he had been surprised when he cried in public: “You don’t realise in tragedies how things catch up with you.”

However, he would not mention Sala in his team talk before Saturday’s game at Southampton. “You have to get on … I don’t think you ever forget things like this. There are times during the day when I think about it. You have to move on.”

Facebook Twitter Pinterest Flowers, cards and messages are left in tribute to Emiliano Sala outside Cardiff City stadium. Photograph: Aaron Chown/PA

Warnock declined to talk about Nantes’ demand for the first instalment of Sala’s £15m transfer fee, saying: “Any sensible journalist will have their own view on that without me commenting.”

The aircraft carrying Sala and Ibbotson, crashed on 21 January, en route from Nantes to Cardiff. The body was recovered from the sea north of Guernsey and formally identified by the Dorset coroner.

Several top players paid tribute to Sala, including Manchester City’s Sergio Agüero, a fellow Argentinian, tweeted: “Rest in peace, Emiliano. My condolences to his friends and family.”

Argentina’s president, Mauricio Macri, also tweeted his condolences to Sala’s family, adding: “We are with you.” Last month Macri had joined calls for the official search for Sala and Ibbotson to resume.

David Mearns, a shipwreck expert who led a private search for the plane, tweeted: “Rest in Peace Emiliano. I was glad to provide some small comfort to … the whole Sala family during the past two weeks but my heart goes out to the family and friends of David Ibbotson whose loss is the same.”

Dorset police said the families of Sala and Ibbotson would continue to be supported by family liaison officers.

The wreckage of the Piper Malibu N264DB that was carrying the two men was found on Sunday. Poor weather made efforts to recover the body seen inside more difficult.

Sala had recently been signed by Cardiff City and was flying to south Wales from Nantes after saying goodbye to old friends and teammates when the crash occurred.

Dorset police said the coroner would continue to investigate the circumstances of Sala’s death, supported by its officers.

The Air Accidents Investigation Branch said the operation to recover Sala’s body was “carried out in as dignified a way as possible” in challenging conditions. However, ongoing poor weather meant it had decided not to continue efforts to raise the plane, which it had surveyed using a remotely operated vehicle.

It said the video footage captured by the ROV was expected to provide valuable evidence for its investigation. An interim report on the crash was expected by 21 February.