The Blanco rider, who rode to a one-second win on the opening stage in Malaysia, beat Andrea Guardini (Astana), Aidis Kruopis (Orica-GreenEdge) and Bryan Coquard (Europcar).
After a shorter 116km run from Serdang, Bos began his sprint 200m from the finish in Kuala Kangsar after being set up by his team-mates.
He now leads the GC by 10 seconds from Guardini, with Meiyin Wang (Hengxiang) a second further back and Coquard and Anuar Manan (Baku Cycling Project) three seconds behind him.
The latter duo is two seconds ahead of Kruopis.
Saturday’s stage three sees the riders race over 145.4km from Sungai Siput to Cameron Highlands, with the race having 10 stages in all and finishing with the Kuala Terengganu Loop.