Ronaldo, who overtook former Real Madrid teammate Iker Casillas, stole an undeserved winner for United on Wednesday after a clever layoff from Jesse Lingard.
United are joint second in Group F on three points, level with Young Boys, who beat them on opening day. Atalanta are top on four after edging the Swiss side 1-0.
Elsewhere, Barcelona suffered a second straight 3-0 loss in the Champions League group stage as they were well beaten by Benfica in Lisbon on Wednesday.
Ronald Koeman’s men, who lost their opener to Bayern Munich, now desperately need two wins in their upcoming games against Dynamo Kyiv to boost their hopes of getting out of Group E.
Federico Chiesa’s goal at the start of the second half gave Juventus a 1-0 win over holders Chelsea.
It is a second straight defeat for Chelsea after their loss to Manchester City at the weekend and it leaves Thomas Tuchel’s team three points behind leaders Juventus in Champions League Group H.
Meanwhile, devastating Bayern Munich confirmed their status among the favourites for the Champions League with a 5-0 demolition of Dynamo Kyiv.
Robert Lewandowski’s with a half double, Serge Gnabry, Leroy Sane and Eric Maxim Choupo-Moting after the break kept Bayern perfect in Group E while Barcelona’s struggles continued with a second 3-0 loss, this time away to Benfica.
Atalanta 1-0 Young Boys
Zenit 4-0 Malmo FF
Bayern Munich 5-0 Dynamo Kyiv
Benfica 3-0 Barcelona
Manchester United 2-1 Villarreal
Salzburg 2-1 Lille
Wolfsburg 1-1 Sevilla
Juventus 1-0 Chelsea