The Red Devils, who hastily arranged the rematch after the Indonesia leg of their tour was cancelled due to the terrorist attacks in Jakarta, surrendered a two goal lead against the Malaysian outfit on Saturday, only for new signing Owen to emerge from the substitutes' bench and snatch the winner.
However, Monday's encounter was a more straightforward affair for the Premier League champions, taking the lead in the 11th minute and doubling it soon after.
Fabio da Silva’s left-wing centre found Darren Fletcher at the far post, with the midfielder pulling the ball back for Federico Macheda to fire home United’s opener.
And Owen then grabbed his side’s swift second, tapping home a Zoran Tosic cross.
Unlike on Saturday, Manchester United did not relinquish their lead, with Ben Foster and second-half substitute Tomasz Kuszczak both keeping clean sheets.
But, disappointingly for the tourists, Sir Alex Ferguson's side failed to extend their early lead, despite cameo appearances from Wayne Rooney, Nani and Dimitar Berbatov.
United’s next friendly is against FC Seoul on Friday.
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