The win will be welcomed by Malaysia as they prepare for the AFF Championship in November.
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.
Malaysia had a second goal, scored by Wan Zack Haikal Wan Nor in the 54th minute, ruled out for offside.
Source: the-afc.com