Cardiff were the better side in the opening stages and only a superb last-ditch challenge from Michael Hector prevented Robert Glatzel from prodding into an empty net.
Fulham went close to taking the lead in first-half stoppage time when Tom Cairney's curled effort from 25 yards clipped the outside of Alex Smithies' right-hand post.
They did forge ahead four minutes after the restart, Onomah waltzing past three Cardiff defenders inside the penalty area before coolly finishing past Smithies.
Kebano then whipped home a wonderful free-kick in stoppage time to give Scott Parker's side a healthy advantage ahead of the second leg at Craven Cottage on Thursday.
The Argentine striker died in a plane crash in January 2019 while travelling across the English channel to the Welsh side and a legal battle has ensued over the outstanding transfer fees owed.
Cardiff have argued that they were not liable for the fee because the 28-year-old was not officially their player and refused to make any interim payments as they stated the deal was not legally binding.
FIFA disagreed, however, and the appeal was heard by a three-man Court of Arbitration for Sport (CAS) panel earlier this year, who rejected the appeal.
In a statement, Cardiff expressed disappointment in the ruling and confirmed their intention to lodge an appeal – adding that they will take their own legal action should they fail.
"Cardiff City is disappointed by the decision of the Court of Arbitration for Sport," Friday's statement read.
"The award fails to decide the crucial question of FC Nantes' (and its agents') liability for the crash, which will therefore have to be decided in another forum.
"Once the club's lawyers have digested the reasons for the decision we expect to appeal and will not be making any payments to FC Nantes in the meanwhile.
"If those appeals are unsuccessful and the club is liable to pay the transfer fee, the club will take legal action against those responsible for the crash for damages to recover its losses. This will include FC Nantes, and its agents.
"All our thoughts must continue to be with Emiliano's family, who are now supported financially by the trust the club put in place for them."
On the ruling, CAS said: "After taking into due consideration all the evidence produced and all the arguments put forward by both clubs, the Cas panel found the player's transfer from FC Nantes to Cardiff City FC to have been completed.
"And because the conditions set out in the transfer agreement were fulfilled prior to the player's death, FC Nantes' claim for the first instalment of the transfer fee in the amount of 6m euros was upheld."
Henderson, 67, was last month found guilty of endangering the safety of an aircraft.
Sala was on his way to Cardiff City on January 21, 2019, after signing from Ligue 1 club Nantes for £15million (€20m) when his plane came down over the English Channel, killing the striker, 28, and the pilot, Ibbotson, 59.
The court was previously told Henderson arranged the flight with football agent William McKay and asked Mr Ibbotson to fly the plane as he was in Paris on holiday.
Mr Ibbotson – who did not hold a commercial pilot's licence – was not qualified to fly at night and his rating to fly the single-engine Piper Malibu had expired.
A jury of seven men and five women were told that moments after finding out about the incident, Henderson contacted numerous people to ask them to stay silent, saying it would "open a can of worms".
The jury took seven and a half hours to come to a verdict before Henderson was convicted at Cardiff Crown Court, where he returned on Friday to be sentenced.
Henderson was given 18 months for endangering the safety of an aircraft, along with a three-month sentence to be served concurrently for attempting to discharge a passenger.
With the coronavirus infection rate in the country at just under 550 cases per 100,000 people and rising, the government opted for an open-ended ban on crowds beginning with the festive season.
Earlier on Monday, Cardiff City's scheduled Boxing Day game against Coventry City in the Championship was postponed, the second consecutive Bluebirds game called off due to coronavirus cases among the squad and staff.
Several other fixtures across multiple sports also have been called off amid COVID-19 concerns.
Amid that environment, Wales economy minister Vaughan Gething announced the new restrictions late on Monday.
"Sporting events over the Christmas period are one of the big highlights of the year," Gething said in a release. "Unfortunately, the new Omicron variant is a significant development in the pandemic and could cause a large number of infections.
"We need to do everything we can to protect people’s health and control the spread of this awful virus.
"Throughout the pandemic we have followed scientific and public health advice to keep people safe. The advice is clear – we need to act now in response to the threat of Omicron. We are giving people as much notice of these decisions as we can.
"Crowds will come back as soon as possible. We want everyone to be here to enjoy their favourite sports."
In addition to league competition, the new restrictions likely will affect FA Cup play. Swansea City are set to host Southampton in a third-round tie on January 8, with Cardiff City to host Preston North End the following day.
