The former South Africa under-20 coach succeeds Moses Maliehe, who resigned recently due to continuous ill health.
Lesotho play Ethiopia away on September 4 and at home on September 8 with the winners advancing to the group phase, which begins next March.
Senong must also prepare Likuena (the Crocodiles) for 2021 Africa Cup of Nations qualifiers away to Sierra Leone and at home to Nigeria during November.
The 38-year-old has assisted South Africa coaches Ephraim ‘Shakes’ Mashaba and Stuart Baxter, but this will be his first senior post.
He also worked under coach Pitso Mosimane at Mamelodi Sundowns, who have been South African champions four times in the past six seasons.
Lesotho, who have never qualified for the World Cup or Cup of Nations, are ranked 40th in Africa and 144th in the world.
