The Argentine ace netted in the 71st and 80th minutes as the Catalan giants' blushes were saved against a Spartak outfit who conceded first before coming back to take a 2-1 lead.
Cristian Tello's 14th minute finish was cancelled out by Dani Alves' own-goal on the half-hour mark prior to Romulo edging the Russians ahead but enter Messi who did what was required of him once again to secure maximum points for Tito Vilanova's side.
The Blues young Brazilian midfielder Oscar scored a double in two minutes just after the midway stage of the first half - the second an absolute stunner - before Arturo Vidal and Fabio Quagliarella saved the day for Juventus.
Sir Alex Ferguson became the first manager to oversee 100 wins in the Champions League as Manchester United defeated Galatasaray 1-0 at Old Trafford courtesy of Michael Carrick's seventh minute goal whilst Scottish giants Celtic were held to a 0-0 draw by Portugal's Benfica.
In the remaining matches, Shakhtar Donetsk beat newcomers Nordsjaelland 2-0 in Ukraine and Romanian outfit CFR Cluj kicked off their campaign with a 2-0 triumph at Sporting Braga.
2012/13 Champions League scores
Shakhtar Donetsk (UKR): 2 (Henrik Mkhitaryan 44'/76') Nordsjaelland (DEN): 0 Donbass Arena, Donetsk, Ukraine - 51,624