The win put Kenya on course to defending the Singapore title they won last season.
Gordon Langkilde put Samoa ahead with a converted try before Amonde weaved through the Pacific Islanders defence to draw Innocent Simuyu's charges level at the stroke of half-time.
Second half tries by Billy "The Kid" Odhiambo and Nelson Oyoo helped Shujaa see off Samoa, although the Islanders were undone by two yellow cards to their players in a span of two minutes.
