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The Blues beat their Spanish opponents 6-5 on penalties following a pulsating 1-1 draw in regulation and extra time.
Hudson-Odoi was handed a starting role by manager Thomas Tuchel and he has a lively presence until he was substituted in the 82nd minute.
Hakim Ziyech opened the scoring for Chelsea in the first half but Villarreal rallied back to restore parity in the second half, thanks to a well-taken strike from Gerard Moreno.
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With no winner emerging from open play, the game had to be decided through the lottery of penalties in Belfast.
Kepa Arrizabalaga, who replaced Edouard Mendy in the last minute of extra-time, was the hero after saving two penalties.
The Spain international stopped the efforts of Aissa Mandi and Raul Albiol as Chelsea triumphed 6-5 on penalties to win the Super Cup.
Meanwhile, Hudson-Odoi has now won every major European trophy at club level, having already won the UEFA Champions League and the UEFA Europa League.
The 20-year-old arrived in Ghana earlier in June and spent a week fraternising with the locals and meeting some key people.
The winger has Ghanaian parents and his father, Bismark Odoi, played for Ghana Premier League giants Hearts of Oak in the 90s before relocating to England.
While in Ghana, he paid a courtesy call on President Nana Akufo-Addo at the Jubilee House, where the possibility of a nationality switch was discussed.
He also met with Sports Minister, Mustapha Ussif, and the President of the Ghana Football Association (GFA), Kurt Okraku.
Despite playing three times for England, Hudson-Odoi is still eligible to play for Ghana due to a change in rules by FIFA.