United emerged with a victory at Lincoln Financial Field but laboured in their second pre-season friendly after beating Scottish team Celtic 3-1 last week in Toronto.
The winning goal came in the 76th minute after Danny Welbeck intercepted a sloppy pass in midfield and ran straight through the defence before passing to Gabriel Obertan who slotted the ball home.
Bulgarian striker Dimitar Berbatov nearly extended United's lead, hitting the crossbar from close range in the 80th minute.
United coach Sir Alex Ferguson praised Philadelphia's aggressive play.
"It was the sort of game we needed," Ferguson told reporters after the match. "They were very good opponents."
Ferguson said that United was flush with youthful talent this season.
He said he would consider loaning Welbeck and Tom Cleverly, who played in central midfield on Wednesday night, to other Premier League clubs to give the youngsters more competitive experience.
The Scot declined to comment on speculation that central defender Nemanja Vidic, resting after his World Cup exploits with Serbia, might leave United, saying, "I can't clarify it at all."
Asked if he would play for the Manchester team this season, Ferguson replied, "I believe so."
United started the game with the attacking trio of Federico Macheda, Welbeck and Obertan but while the first half saw the English team dominate possession, their young strikers failed to convert a series of good chances.
The best chance of the first half fell to Welbeck after 36 minutes but he hit his close-range shot directly at the goalkeeper.
Five minutes later, Union's in-form French striker Sebastien Le Toux found himself through on goal but dragged his effort wide.
The Union, in their first MLS season, pressed United hard in the second half and had several chances to take the lead.
The Philadelphia team enjoyed an unexpected victory last week when they beat Celtic 1-0.
With the game still goalless after an hour, United made several substitutions, bringing on Berbatov for Macheda and Darren Fletcher for veteran midfielder Paul Scholes.
The Union could have leveled the game in the 89th minute when Andrew Jacobson skied the ball over the bar from just a couple of yards out.
The game's final chance came in injury time to United's Ritchie De Laet, who tried to chip the keeper but saw his effort saved.
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