But, after Daniel Sturridge nodded back a corner and Jack Wilshere helped it on, Smalling swept in the winner.
And perhaps Ferguson deliberately made a point by including the likes of Tomasz Kuszczak, Chris Smalling, Rafael and Federico Macheda.
Hernandez is United's second capture for next season having reached agreement to sign defender Chris Smalling from Fulham in January.
"We've spent a lot of time away from our families and grown closer as a squad, " centre-back Chris Smalling told BBC Sport.
Chances were at a premium, with Bursaspor failing to trouble a sound-looking United defence in which Smalling more than held his own.
"Roy is one of the best managers around, " said 20-year-old Smalling, who will join Manchester United this summer after impressing Sir Alex Ferguson.
Zamora doubled the lead by heading in another Riise centre but Alexander Frei pulled one back from the spot after Chris Smalling handled.
Chris Smalling has done incredibly well in his short spell in the time, but how Ferguson would love Vidic alongside him on Sunday.
Hughton's sentiments are likely to be echoed by Sunderland's Steve Bruce and Manchester United's Sir Alex Ferguson, respectively the managers of Henderson and Smalling at club level.
It was harsh on England but they restored their lead when centre-back Smalling proved to be in the right place at the right time to score late on.
"In every round we've managed to surpass expectations and each time you go a step further you become more and more hungry to go all the way, " explained Smalling.
Smalling handled an Almerares cross and, after some confusion over whether Johannesson had pointed for a corner or a penalty, Frei lashed his spot-kick into the top left-hand corner.
Van der Sar was equal to Petrov's free-kick, Johan Elmander had a shot blocked by Patrice Evra and the backline, well led by Chris Smalling, was forced to repel a wave of Bolton attacks.
Bursaspor created a moment of danger when Sercan Yildirim broke down the left and slipped the ball past the covering Smalling but there was nobody in the six-yard box to convert it into a real chance.
Newcastle's Carroll was one of four new picks for Fabio Capello's squad, along with Cardiff striker Jay Bothroyd, Manchester United defender Chris Smalling and Sunderland midfielder Jordan Henderson, who was instrumental as the Black Cats won at Chelsea.
Hargreaves' fitness is one of the matters Ferguson will give thought to this summer as he looks to reshape a squad that has already been bolstered by the signings of Javier Hernandez and Chris Smalling, with more set to follow.
Smalling is a real talent in the making, but he is inexperienced and, with Rio Ferdinand still out, you could now be looking at a United back four of Patrice Evra (if he's fit), Smalling, Wes Brown and John O'Shea.
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