
Despite playing without suspended regulars La’Vere Corbin-Ong, Syamer Kutty Abba and Mohamadou Sumareh, Tan Cheng Hoe’s men started on the front-foot and kept probing throughout the first half.
Substitute Safawi, who came on for Brendan Gan at halftime, won and converted the spotkick in the 52nd minute to end Malaysia’s two-match winless run in the second round.
Victory means Malaysia finish third in Group G on 12 points – three above their opponents – to guarantee a place among the 24 teams in the final qualifying round which starts in November.
The 24 nations will be divided into six groups of four to play home and away round-robin matches.
The top two in each group will advance to the Asian Cup in China, where they will be joined by the 12 countries already qualified from this round.