Liberian striker Edward Junior Wilson struck in the 24th and 64th minutes while Titus Bonai found the target for the Indonesian Premier League champions in the 47th minute at Agus Salim Stadium.
Bineesh Balan pulled a goal back in the 49th minute for Churchill, who fielded a second string team for the inconsequential match by leaving out key players in view of their title race for the I-League.
The match also saw Churchill's Naveen Kumar being sent off in the first minute of the second half.
Wilson opened the scoring with a superb solo goal midway through the first half before Bonai's free-kick doubled Semen Padang's lead at the start of the second half.
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And after Bineesh Balan pulled a goal back for Churchill Brothers, another eye-catching solo effort from Wilson sealed the home side's fourth win of their campaign.
Despite Semen Padang already having secured their place in the last 16 as Group E winners following an impressive maiden AFC Cup campaign, the home side dominated for long periods of the first half against already-eliminated Churchill Brothers with captain Ellie Aiboy, Vendry Mofu, Wilson and Bonai all coming close to a breakthrough for the home side.