Mr Musyoka is currently in Germany and expressed his sadness upon receiving the news.
"In the departure of Hon. Nyenze, the Wiper Democratic Movement-Kenya fraternity in particular, and Kenyans, in general, have lost a great leader.
"As Leader of Minority in the 11th Parliament, Hon. Nyenze served the country with great commitment and dedication.
"His non-confrontational, gentlemanly mien was a great asset in helping to build bridges among political protagonists," wrote Kalonzo.
He also described the deceased as a candid politician who never shied away from articulating his political convictions.
The Wiper Party leader fondly remembered the nickname Nyenze had been given by his constituents in the early days of his career and termed his demise a huge loss to the constituency.
"In Kitui West where he was immensely popular, he was nicknamed, "Shabiki" (Fan), a term coined from the early years of his political career when he used to mobilize his political supporters particularly the youth using "Shabiki" as his rallying call.
"In the passing of Francis, I, too, have personally been dealt a big blow since he was also a great family friend," added the NASA co-principal.
President Uhuru Kenyatta also mourned the legislator describing him as a leader who served his constituents with commitment and dedication.
The Head of State added that the late MP always championed national interests and would never allow narrow selfish interests jeopardize the unity of Kenyans.
“I have known the late Nyenze since the time he was a Cabinet Minister under President Moi’s administration, he was always keen on preserving our unity and nationhood.
"I urge all of us to emulate his leadership style,” stated President Kenyatta.
Nyenze passed away at a Nairobi hospital on Wednesday after a battle with cancer.