Some of the catcalls were aimed at referee Alan Wiley, but plenty were aimed at the Magpies, still without a win in 2005-06.
Substitute Charles N'Zogbia's late free-kick saw Souness' men salvage something from the game, with Brian McBride having given Fulham an early lead.
Scott Parker was also sent off as St James' Park witnessed another eventful - but ultimately disappointing - Premiership fixture.
Owen was given a huge ovation when the teams were read out before kick-off, though Owen-mania had not reached London with Fulham bringing to St James' Park one of the smallest away followings in the Premiership for several years.
And the United fans almost had something to cheer in the third minute, when Albert Luque played a perfect ball in behind the Fulham defence from the left wing. Alan Shearer - looking for his first league goal since February - broke into the box on the right and shot just wide of Tony Warner's goal from a tight angle.
Newcastle started brightly, but it was not long before there were chants of "Souness out" from the small pocket of Fulham fans after their team took a 13th-minute lead.
Steven Taylor's back pass to Shay Given was cut out by Tomasz Radzinski, and the Canadian quickly found Luis Boa Morte just inside the United box.
Boa Morte - a player Souness attempted to sign in the summer - centred for McBride, who had a simple tap-in for his third goal of the season.
The optimism and expectancy which had filled St James' Park at the start soon drained away.
Carlos Bocanegra was booked in the 20th minute after crudely stopping Owen in his tracks as the Magpies looked to get themselves back on level terms.
Without Emre and Kieron Dyer through injury - and new signing Nolberto Solano through the second game of a three-match suspension - Souness opted to draft Stephen Carr into midfield, the Republic of Ireland full-back lining up on the right wing.
In the centre were Parker and Amady Faye, though the wisdom of playing the limited Faye in front of Parker in the anchor role looked questionable.
Luque looked the only midfielder capable of opening Fulham up, but the Spaniard had not seen much of the ball as the half-hour mark approached.
In the 30th minute Owen should have opened his United account. Luque swung in a corner from the right which found the England striker unmarked at the far post, but the bounce caught him out and the ball squirmed through his legs.
Papa Bouba Diop then forced an unconventional save from Given, with the Irishman saving with his legs as Luque received treatment off the field. The former Deoprtivo La Coruna man was replaced by N'Zogbia.
As the half wore on it was difficult to see how United's patched-up midfield was going to supply Shearer and Owen with any kind of service, with Faye in particular lacking any composure on the ball and the industrious Parker doing the jobs of two men.
Things got worse for United as Steven Taylor was forced off at the break after colliding with a post making a goal line save from Radzinski. His replacement was Lee Bowyer, himself only half fit after suffering an abductor strain against Manchester United.
Given saved well from Radzinski two minutes into the half, as Fulham pressed for a second goal against a Newcastle side lacking shape and organisation.
After a spell of pressure St James' Park rallied behind Souness' team, but the Magpies still did not look capable of ending their Premiership goal drought against a team which had conceded six goals in its previous two away games.
Ironically, the last goal scored by a United player had come at Craven Cottage in early May, when 72nd-minute substitute Lee Clark - on for the woeful Faye - was still a Fulham player.
Carr saw a long-range effort come back off the crossbar in the 75th minute, and three minutes later the breakthrough came after Owen was felled by Boa Morte on the right side of the box.
N'Zogbia stepped up and flighted a left-foot shot into the far corner to score his team's first goal of the campaign.
The game then unravelled further, with Parker being given his second yellow card after pulling back Claus Jensen.
Man of the Match: Luis Boa Morte
The Portuguese winger showed Newcastle exactly what they missed out on when they refused to meet Fulham's £6million asking price during the summer. His pace and creativity - two things United lacked - were a constant threat to the hosts.