While the failure of the Premier League title rivals to progress means the end of English representation, Spain has three sides in Friday's draw for the quarter and semi-finals with Atletico Madrid and Valencia joining Bilbao.
United and City had parachuted into the second-tier competition after group-stage exits from the Champions League and boasted much bigger resources than their conquerors. But the manner of the exits could not have been more different.
United, who this time last year were well on their way to the Champions League final, were outplayed in both legs by Bilbao, losing 2-1 in Spain and 5-3 overall.
City clawed their way back from 2-0 down on the night with three goals in the last half-hour to win 3-2 at home to Sporting but went out on away goals after a 3-3 aggregate result.
Their recovery was at Eastlands was breathtaking as two goals by Sergio Aguero and a Mario Balotelli penalty put them on the verge of a remarkable comeback.
A fairytale ending was millimetres away when goalkeeper Joe Hart's header whizzed just wide in the last minute of stoppage-time after his opposite number Rui Patricio tipped it past the far post.
In the end, first-half goals from Matias Fernandez and Ricky van Wolfswinkel were enough for Sporting after their 1-0 first-leg win as City were left contemplating the two very different performances they had given either side of the break.
"It was really a strange game," defender Kolo Toure told ESPN. "I think we gave it [our] all. Joe had a great header at the end and it's a very unlucky day for us."
Manager Roberto Mancini had been left angrily shaking his head when Balotelli, the villain of City's departure at the same stage last season when he was sent off against Dynamo Kiev, needlessly gave away the free-kick that led to the opener.
But while Mancini said he was disappointed at yet another example of the Italian striker's ill discipline, he did not blame him for the defeat this time.
"It is not his fault we lost this game, I'm the manager, it's my fault," he said.
City's verve was not mirrored by a poor United who were undone by a stunning first-half volley from Fernando Llorente and a deflected strike from Oscar de Marcos.
United forward Wayne Rooney scored a superb 80th-minute consolation goal but the damage was already done as the enthusiasm and skill of La Liga's seventh-placed side proved too much for the English champions.
"I don't think we can complain," United manager Sir Alex Ferguson told Channel Five television. "There are always lessons in every football match whether you win or lose."
"It's the disappointment more than anything that we haven't progressed in the Champions League and we're out of the Europa League now."
While the two English clubs are left to give their undivided attention to domestic matters, the European adventure continues for others including Germany's
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