Owen, a free transfer arrival from Newcastle United earlier this month, scored from close range on 85 minutes having started life in United colours as a 60th minute replacement for Wayne Rooney
Twenty four hours after United's four-game tour was marred by the bombings in Jakarta, which led to the club cancelling their planned fixture in the Indonesian capital on Monday, Owen, who was afforded a Ronaldo-like reception by the Malaysian supporters, ensured that his new employers avoided an embarrassing opening to their tour on the pitch with his goal.
United will face the Malaysians again on Monday after confirming that they will remain in Kuala Lumpur and Owen is likely to start in the rematch according to manager Sir Alex Ferguson.
Ferguson said: "Michael was never going to start this game, but I will definitely make changes on Monday and it will be a totally different team that starts.
"His goal was a typical Michael Owen goal, though. This was only a friendly game and the time to judge will be in the new season, but I am looking for him to score goals for us and I'm sure he will give us a good contribution.
"He is a high profile player, so wearing the number seven shirt won't be a problem for him. He can handle that."
United, performing for the first time since the Champions League final defeat against Barcelona 52 days ago, began life without Cristiano Ronaldo impressively by racing into an early 2-0 lead against the Malaysians in stifling humidity in Kuala Lumpur's Bukit Jalil Stadium.
Deploying a forward line of Wayne Rooney
and Dimitar Berbatov following the summer departures of Ronaldo and Carlos Tevez, Ferguson saw Rooney open the scoring on eight minutes when he netted from close range after Berbatov's volley from Darron Gibson's shot had been parried by goalkeeper Farizal Marlias.
When Nani doubled United's lead on 28 minutes, shortly after a long-range effort from Paul Scholes, the tour curtain-raiser appeared to be adhering to the script.
But an error of judgement by goalkeeper Edwin van der Sar led to Amri Yahyah scoring for the hosts with a speculative lob just before half-time.
Van der Sar was replaced by Ben Foster at the interval, but the England goalkeeper made an even worse mistake than his Dutch team-mate on 52 minutes when he completely missed Gibson's back-pass, allowing Yahyah to sneak in for an equaliser.
The introduction of Owen on the hour mark prompted a wildly excited response from the 80,000 supporters inside the ground and the 29-year-old did not disappoint, scoring the winner five minutes from full-time when he pounced on a loose ball on the edge of the penalty area before shooting from 18 yards.
United have rejected appeals by Indonesian officials to show defiance in the face of terrorism by going ahead with their planned game in Jakarta on Monday.
Nine people were killed in suicide bombings at Jakarta's Marriott and Ritz-Carlton Hotels, the hotel due to host United from Saturday evening.
Indonesian Presidential spokesperson Dino Patti Djalal said: "There is no more powerful message to the world than to continue with the Jakarta match as planned.
"Of all the great feats that have been, and will be, achieved by Manchester United as a great football team with a heart, this one – proceeding with the match in Jakarta as a measure of solidarity – will be long remembered by history."
United, however, have confirmed their decision not to travel to Jakarta will stand and, despite an offer from the Australian Football Federation to stage a game in Sydney on Monday, the club will remain in Kuala Lumpur until Wednesday before flying to Seoul for the next leg of the Far East tour.
MANCHESTER UNITED (4-4-2): Van der Sar (Foster h-t); O'Shea, Ferdinand (Brown 60), Evans, Evra (Fabio 60); Gibson, Scholes (Tosic 60), Anderson (Giggs 76), Nani; Berbatov (Macheda 76), Rooney (Owen 60). Subs: Neville ends