The Colombian climber’s late solo attack on the steep Genting Highlands finish saw him move clear of Orica-GreenEdge rider Pieter Weening inside the closing two kilometres to take the lead in the general classification.
Weening had sparked the initial attack three kilometres earlier, but was able to hold on for second, ultimately finishing 26 seconds behind Arredondo.
Victor Nino Corredor of RTS finished third on the 110.3km stage, with the arduous climbs picking off riders one by one from the back of the leading group.
“I need to thank all my teammates,” Arredondo said. “This is a very big victory for us.
“This win is very important for us because we are a little team, and sharing the road with other pro teams is very important.
“We are an Asian team and to win the most beautiful stage for us is incredible. It’s like a dream come true.”
The tour continues with stage six on Tuesday, taking the competitors from Mentakab to Kuantan, with the 10th and final stage coming on Saturday with a finish in Kuala Terengganu.