It was Goncalves' first appearance under Jefferies, who had vowed not to play him while he refused to sign a new deal with the club, and his selection followed reports that permission to field him had been sought from majority shareholder Vladimir Romanov.
Jefferies, who succeeded Csaba Laszlo in January, denied any knowledge of that but revealed he had discussed the matter with Metlitksi.
"I report to the sporting director and I told him the situation, that we needed to play him," Jefferies said following his side's 1-0 defeat. "He agreed and there was no problem.
"Everybody understands that it was a necessity today because of the injuries we've had.
"If I had somebody else fit, he wouldn't have played. If he hadn't have played today God knows who I would've played in there."
Jefferies denied previously stating Goncalves would not be selected until he extended his contract, which expires this summer.
And asked if Goncalves would remain part of his plans for the rest of the season, Jefferies added: "We'll obviously try to negotiate and get this thing resolved.
"If we don't, well wait and see. It's better to concentrate on players who want to be here."