UAE won the toss and opted to bat, scoring a target of 267 runs for the hosts to chase thanks to S Maqsood, who top scored with 83 runs.
A A Khan (54) and Karim Khan (39) were equally devastating with the bat as the Malaysian fielders had a tough time trying to contain the UAE batsmen.
Maqsood, who faced 97 balls, hit three boundaries and four sixes before eventually falling to a catch by M Muniandy.
The Malaysian bowling attack which was led by skipper Suresh Navaratnam proved expensive as they gave away a total of 23 extras. Suresh was the best Malaysian bowler with figures of four for 46.
Malaysia started off brightly but their three top batsmen Rohan Selvaratnam (40), Rakesh Mahdevan (68) and Sarath Jayawardhene (51) were all victims of run outs.
In the end, Malaysia could only score 206 runs, falling short of the UAE total by 61 runs.
UAE will now take on Kuwait in the semifinals at the same venue.
Kuwait defeated a spirited Afghanistan side by 49 runs in their quarter-final match.
Oman had the easiest of the quarterfinal matches as they defeated Bhutan by 10 wickets. Bhutan, who batted first, could only manage a paltry 70 runs and Oman surpassed the total in only 4.4 overs with A Illayas hitting 50.
In the semis Oman will meet Qatar, who dashed the hopes of Nepal with a four-wicket victory.
Quarterfinal results: Oman bt Bhutan by 10 wickets. Bhutan 70 in 40.3 overs (M Adhikari 14, L Yonten 2-49); Oman 71 for no loss in 4.4 overs ( A Illayas 50, H Mehta 4-6)
Qatar bt Nepal by four wickets. Nepal 164 for 9 in 50 overs; Qatar 165 for 6
Kuwait bt Afghanistan by 49 runs. Kuwait 242 for 10 in 49.4 overs (K Butt 117, M Ali 3-38); Afghanistan 193 in 44.2 overs (N Khan 63, N Khan 4-27)
UAE bt Malaysia by 61 runs. UAE 267 in 49.5 overs (S Maqsood 83, S Maqsood 4-43); Malaysia 206 in 47.2 overs (M Rakesh 68, Suresh Navaratnam 4-46).