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."
Hearts' injury list grew even further when captain Michael Stewart was forced to pull out of the side after the warm-up.
The midfielder picked up a calf strain on Thursday and it had been hoped he would shake it off.
"By the time he was on the bus coming up here and warming up it just stiffened up," said Jefferies, who hailed the performance of stand-in Paul Mulrooney.
"He (Mulrooney) covered every blade of grass, tackled well, competed, passed it quite well.
"What a terrific plus for us today when you see a young kid like that."
United boss Peter Houston admitted he feared his side would be made to pay for their wasteful finishing before Morgaro Gomis sealed a 1-0 victory.
Gomis' 77th-minute winner, which found the net via a huge deflection, was the midfielder's third goal in two games.
Houston said: "We must have a midfield player in the box and Morgaro has taken me to task on that one and he's become a machine.
"I'm delighted with the three points today because you never get an easy game against a Hearts team."
Houston felt his side should have had a first-half penalty when the ball appeared to strike David Obua's hand.
"I was at pains to wonder why we never got the penalty kick there," he said.
United left-back Paul Dixon was forced off in the second half with a problem with his right ankle, having sat out games recently with a knock to his left one.
"Hopefully it's not as bad but hopefully the next 48 hours we'll be able to tell," Houston said.
Sunday's win lifted United back up above Hibernian into third place, 11 points clear of their sixth-placed opponents.
Houston admitted the race to finish behind the Old Firm was looking a three-club affair but added: "I think there'll be a lot of twists and turns between now and the end of the season because we're going to be playing each other."
Source: Team Talk
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