The Gulf Cup winners, coached by Frenchman Bruno Metsu, demonstrated their superiority on a heavy pitch against a home side that goes into the Asian Cup next month as the lowest-ranked team in the 16-nation competition.
UAE's towering attacker Faisal Khalil netted the opening goal in the ninth minute, pouncing on a loose ball after Nawas Mubarak's header had grazed the post off a cross from right flanker Khalead Darwish.
The home side then enjoyed a good spell, forcing the visitors on to the defensive, but their efforts lacked goals.
Eight minutes after the interval, UAE, who will play defending champions Japan, Asian Games gold medallists Qatar and hosts Vietnam in Group B of the Asian Cup next month, added a second through their star striker Ismail Mattar, from point blank range after the Malaysian defence failed to clear an attack. Much to the home side's disappointment, Mohamed Al Shihi capitalised on another lapse of concentration to convert Ismail's cross from the right to widen the gap in the 67th minute.
Malaysia's consolation goal came at the death, when Akmal Rizal Ahmad Rakhli tapped home a pass from substitute Eddy Helmi Manan.
Metsu was happy with the result.
"I was satisfied with the outcome, having given more than 20 players a chance to play tonight," he said.
" It's important for the players to find a rhythm ahead of the tournament and I intend to the first set of players maybe up to one hour of playing time in our next friendly match."
Metsu's opposite number, Norizan Bakar, said: "We know we need to play stronger sides in order to improve. We lost because we got caught while trying to play short passes."
Malaysia who on Monday had crushed Cambodia 6-0, are grouped with three-time winners Iran, 2004 runners-up China and Uzbekistan in Group C of the Asian Cup.