The 19-year-old Willemse was again impressive as he dictated play and helped the South African side to a narrow win over their Australian visitors as both sides scored three tries.
Dewaldt Duvenage, Wilko Louw and Springbok wing Raymond Ruhle went over for the hosts, who opened up an 18-0 lead but conceded tries either side of halftime to Caleb Timu and Alex Mafi.
Filipo Daugunu scored in the last minute for the Reds to make for a frenetic finish but they ran out of time.
The Reds succeeded in reducing the home lead to just four points after Mafi's try but then allowed the Stormers back in front when a clever grubber kick from Craig Barry sent Ruhle over for his try.
Willemse added 10 points with his boot, as he put over two penalties and two conversions.
The Stormers scored the game's first try in the first 15 minutes when Duvenage finished off a counter attack that Ruhle started around the halfway line.
Louw went over not more than 10 minutes later, only for the Reds to force a turnover at the lineout and set up an opportunity for the powerful eighthman Timu to burst over almost under the poles.
The Stormers' halftime 18-7 lead was reduced immediately after the break as the Reds took advantage of a poor clearance and Mafi scored.
However, Willemse got the Stormers back on the front foot with his darting surges, adding weight to suggestions from pundits that he could win a Springbok call-up when England tour South Africa in June.
An over-eager Stormers backline missed out on several late chances to win the game by a bigger margin.
The Cape Town franchise have won three home games this year and lost the other three away. The Reds were beaten for only the second time in five matches.
(Reporting By Mark Gleeson; Editing by Christian Radnedge)
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