However, the 21-year-old midfielder, who plays for Scottish champions Celtic, will still travel with the squad with Belgian Amrouche seeing him as crucial to Kenya's long-term plans.
The east African country has never played at a World Cup and won't make it to next year's finals in Brazil, with a poor run of results having left them bottom of African qualifying Group F, but Amrouche sees hope for the future.
"Victor was unanimously named as stand-in captain by his team mates, but I have made him permanent captain. He deserves it with his good example on and off the pitch," he told reporters on Saturday.
"We are beginning to build a young team for the future. That team will be built around Wanyama," added the coach who gave the armband to Wanyama after stripping the captaincy from forward Dennis Oliech, who was late to arrive at Keya's training camp.
Kenya have only two points from their four group matches behind African champions Nigeria, who they trail by four points, Malawi and Namibia.
The winners of the 10 African groups face a final knockout round of home-and-away games with the five winners qualifying for the finals in Brazil.