The 36-year-old Portuguese football superstar scored a narrow angle goal in the 95th minute at Old Trafford in Manchester to clinch victory for the Red Devils.
In the meantime, Ronaldo tallied 178 Champions League appearances to be the record holder in this field.
The prolific forward has broken former Spanish goalkeeper Iker Casillas' record as the 40-year-old piled up 177 appearances in Europe's top-tier club level tournament.
Villarreal's Paco Alcacer drew first blood at Old Trafford, scoring the opener in the 53rd minute.
But Manchester United's Brazilian left back Alex Telles pulled level in the 60th minute with a left footed volley outside the penalty box.
Bruno Fernandes whipped a cross from a freekick to assist Telles.
Near the end of the match, Ronaldo scored for his team to seal a home win for Manchester United.
Third place Man Utd have three points in Group F led by Atalanta, who have four points after second matches.
Young Boys also racked up three points.
Villarreal have one point in two matches, so the Yellow Submarine are at the bottom of the group without any win.
BENFICA SHOCK BARCELONA
Portugal's Benfica shocked Barcelona 3-0 in a Group E match in Lisbon. Uruguayan forward Darwin Nunez scored two goals, including a late penalty.
Benfica's Portuguese forward Rafa Silva put the ball into Barcelona's net in the second half. In the 87th minute, Barcelona defender Eric Garcia was sent off after a foul. He was previously booked. Barcelona, who last won the Champions League title in 2015, are in poor form in the 2021-22 campaign.
This season, Barca have lost their two Champions League matches to sit in last position in Group E without any points.
Bayern Munich bagged two wins to top Group E with six points.
The German giants hammered Ukraine's Dynamo Kyiv 5-0 in a Wednesday match where Polish star Robert Lewandowski scored two goals.
Benfica are trailing behind the leaders with four points.
Third-place Dynamo Kyiv have one point in two matches.
LILLE LOSE, BUT BURAK YILMAZ GOES DOWN IN HISTORY
France's Lille lost 2-1 to RB Salzburg in a Group G match in Austria.
Victorious Salzburg's forward Karim Adeyemi, 19, converted two penalties successfully in each half for his club. Lille forward Burak Yilmaz scored from a freekick in the 62nd minute, but it was not enough for the French team.
UEFA confirmed that Yilmaz, at 36 years and 76 days old, became the "oldest Turkish goalscorer in the Champions League." Group G is led by Salzburg as the Austrians have four points.
Sevilla and Wolfsburg racked up two points. Lille have one point to be in last spot.
WEDNESDAY'S RESULTS:
Atalanta - Young Boys: 1-0
Zenit - Malmo: 4-0
Bayern Munich - Dynamo Kyiv: 5-0
Benfica - Barcelona: 3-0
Manchester United - Villarreal: 2-1
Wolfsburg - Sevilla: 1-1
Salzburg - Lille: 2-1
Juventus - Chelsea: 1-0
