The win will be welcomed by Malaysia as they prepare for the AFF Championship in November.
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Syafiq struck with what was Malaysia's first effort on goal and head coach Tan Cheng Hoe will be pleased with the win over the higher-ranked Fijians.
Malaysia's FIFA Ranking is 171 with Fiji six spots better.
Tan opted for a bold approach, fielding five Under-23 players in his starting 11 and he would have been pleased with their performance.
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Malaysia had a second goal, scored by Wan Zack Haikal Wan Nor in the 54th minute, ruled out for offside.
Source: the-afc.com