The Europa League represents a new frontier for Manchester United but they have brought old failings with them. An inability to protect a lead and complacency at Old Trafford contributed to their demise in the Champions League. Both made an untimely reappearance as Sir Alex Ferguson's team advanced in defeat and with nerves frayed against Ajax.

United's performance against Frank de Boer's ultimately vibrant side was everything Ferguson had cautioned against before kick-off and Toby Alderweireld's 87th-minute goal raised the spectre of a second early European exit of the season. Not that warnings should have been necessary following the costly Champions League draws at home to Benfica and Basel in the group phase. Phil Jones, one of four members of Stuart Pearce's England squad for Wednesday's Holland friendly to start the game under the watchful eye of the caretaker manager and Harry Redknapp, admitted that "a little bit of complacency crept in and it cost us".

Unlike in the aftermath of Basel and Benfica, however, Ferguson absolved his players of blame for another home performance that exposed the squad's European inexperience. He took full responsibility for a team selection that almost backfired embarrassingly. "It was nervy," the United manager said. "I've got to accept the responsibility tonight myself – playing so many young players in the back four position was a big ask. It was a good opportunity to give Jones and [Chris] Smalling a game. But their lack of experience at pushing up and tightening up a game showed. For a European game it was too much of a risk. We survived it with a bit of luck."

Ajax lacked conviction in Amsterdam last week yet Ferguson had claimed that United could not consider the job done, even with a two-goal cushion and a clean sheet from the first leg. He gambled, however, on fielding a team with an average age of 24 and a defence with an average age of 21.

United set about ending the contest with haste and Nani had tested the goalkeeper Kenneth Vermeer before Javier Hernández extended their aggregate lead to three. Jan Vertonghen, the Ajax captain and centre-half, cost his team with a careless pass that United's captain for the night, Park Ji-sung, intercepted in midfield. The ball broke for Dimitar Berbatov, who swept a fine pass into Hernández, and the Mexico international stepped inside Alderweireld to confirm his returning confidence with a fourth goal in his past four appearances. An Ajax support strong in number and in song was silenced. They won few friends with chants for Luis Suárez, the club's former striker.

United had opportunities to stretch their lead but Rafael da Silva was fortunate his booking for a lunge on Nicolás Lodeiro was not his second of the night after a ludicrous dive inside the Ajax area went unpunished. Once the visitors had settled, however, it was Rafael's twin brother, Fábio, who had the greater problems as Aras Ozbiliz flourished on the right wing and Siem de Jong took the game to United from central midfield.

"I had a feeling we could get a great result before the game," said De Boer. "But we were insecure in our passing in the first half, even with simple passes like the first goal, and even at 3-0 [in the tie] I felt we could threaten United if we performed as we are capable of doing. I am disappointed. The team could have done much more."

The impressive Ozbiliz brought Ajax level with an emphatic finish into the bottom corner of David de Gea's goal from 20 yards, albeit after Lodeiro had escaped with a handball in the buildup. Ajax dominated possession from the half hour onwards and it was not until the introduction of Paul Scholes, Jonny Evans and Danny Welbeck that United displayed the strength and composure in midfield, plus the pace in attack, to regain a modicum of control.

But they were far from home comfortably. Nani struck the bar on the counterattack and De Gea produced a fine reflex save from De Jong's near-post header as Ajax mounted late pressure. It finally told when the central defender Alderweireld powered home a header from Ozbiliz's free-kick at the back post. "The next game is at home against [Athletic] Bilbao and you will see the experienced players back for that," said Ferguson.