In a niggly clash Sporting were level at the break through a Custodio header after which neither side looked capable of going on to secure a win.
The top position means United avoid the Champions League failures who now drop into the competition and instead will face one of the third-placed sides from the UEFA Cup group stage in the last 32.
Graeme Souness found himself down to the bare bones and named his only fit players in the starting line up.
United's only other recognised, fit senior players Andy O'Brien - who had not started since the Carling Cup exit against Chelsea on November 10 - and keeper Steve Harper were on the bench.
Kieron Dyer and Laurent Robert were the latest casualties as United were only able to name five of their seven permitted substitutes.
With Lee Bowyer suspended, Olivier Bernard moved to the left side of midfield and Robbie Elliott returned at left-back, having started only one of the last eight games.
In what was their 64th Fairs/UEFA Cup clash stretching over 36 years, Newcastle were looking for a repeat of the 1969 Fairs Cup winning campaign. After drawing in Lisbon against Sporting a Pop Robson goal at St James' Park secured a 2-1 aggregate victory in the second round.
Sporting almost snatched a second-minute lead only for Mauricio Pinilla to miss the ball following Martinho Paito's left-wing cross.
Yet it was United who stormed in front after five minutes with a rare Craig Bellamy header.
A ball from the right was met by Shola Ameobi, whose flick on saw Bellamy rise above Beto and loop a header over Ricardo in the visitors' goal.
The hard-working Fabio Rochemback showed was the class act in midfield early on and the former Barcelona midfielder struck a 25-yard drive that flashed narrowly wide, as Newcastle struggled to win possession from the confident and fluent passing Lisbon side.
Little was seen of Newcastle until the 21st minute when Darren Ambrose was left with little option other than to try his luck at goal when chasing an Elliott ball over the top and flashed his drive over the bar.
Having been incorrectly called for offside three times, United finally sprung the trap after 24 minutes when Bellamy seized onto a Steven Taylor pass, but Ricardo produced a fine block with his legs to deny the Welshman.
Newcastle collected first-half bookings for Bramble, Ameobi and Aaron Hughes – the last two in the space of 30 crucial seconds in the 38th minute minutes.
Hughes was harshly penalised for an innocuous looking challenge and from the resulting free-kick the unmarked Custodio headed home. It was the first goal United had conceded in the group.
Newcastle started strongly after the break and Ambrose fired in a wicked low free-kick that Ricardo spilled, but the Lisbon defence managed to hack the ball clear.
However, the second half was a largely dull affair as neither side appeared capable of stamping their authority on the game.
Sporting enjoyed a huge amount of possession in the final 20 minutes but, a tame Rochemback free-kick apart, were unable to get past a hard-working United defence and trouble Shay Given.
Worryingly for United Bellamy limped out of action after 80 minutes because of a blow to the back and was replaced by debutant Lewis Guy. The Welshman must now be considered a major doubt for Sunday's trip to Liverpool.
United saw out the three minutes of time added on by keeping the ball in the corner, with Souness sure to be happy with the result and the performance of his inexperienced line-up.