Trailing by two goals against the Italian team that knocked it out of the competition six months ago, the Spanish side found a way back this time.
The ex-Chelsea coach missed his first two league games with the Serie A champions against Parma and his former club Napoli.
Captain Ronaldo, making his 160th international appearance, scored four as Portugal won 5-1 in Vilnius and strengthened their position in Group B after a sluggish start.
Cristiano Ronaldo played a key role in the winning goal and Juventus beat Fiorentina 2-1 to clinch a record-extending eighth straight Serie A title.
After an excellent start, United were undone twice in four minutes by Messi, who first nicked the ball off the careless Ashley Young and then watched as a weak shot from distance squirmed underneath David de Gea.
Manchester United underwhelmed with no registered shots on target in a 0-1 loss to Barcelona in their UEFA Champions League quarter-final first leg clash. Barca's point was an own goal from Man U's Luke Shaw.
Juventus forced to wait at least another week to celebrate their eighth successive Serie A title after second-placed Napoli draw 1-1 at home to 10-man Genoa.
The dispute over the German magazine Der Spiegel articles on tax avoidance by the star footballer went on for two years. On Tuesday, the lawsuit came to an end – in favor of the magazine.
Juventus star fined the same sum imposed on Atletico coach Diego Simeone for same gesture during the round of 16 first-leg game in Spain.
Ronaldo made the breakthrough in the 27th minute, levelled the aggregate score three minutes after halftime with another towering header and blasted home the decisive goal from a penalty with four minutes left to seal a 3-2 overall triumph.
Real Madrid's Champions League reign is over.
The 33-year-old Juventus forward is expected to plead guilty after he struck a deal last year with authorities in Spain to settle the case by paying an 18.8 million euro ($21.4 million) fine and accepting a suspended jail sentence.
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