Ronaldo, playing in his first competitive game in a month, would go on to find the net from the spot minutes later, meaning after 12 penalties in the Champions League, he is the highest scorer of spot-kicks in Europe's premier club competition.
So far Barca have had a flawless start to the season winning their first three league games and beating Juventus 3-0 in their Champions League debut.
Also, John Stones scored twice, as Manchester City built a big lead and essentially walked to a 4-0 win at Feyenoord on Wednesday in UEFA Champions League play. The youngster has enjoyed a flying start to the season, scoring four goals in Madrid's opening six games.
Reigning Ballon d'Or victor Ronaldo scored twice as two-time defending champions Madrid eased past the Cypriot visitors and Ronaldo and Real Madrid have set their sights on a third successive Champions League crown following the win.
"Now we need experience", he said of their attempt to match the likes of Madrid. We finished well and we are happy with that.
"It was a game that we really needed to win".
"John played well and while he scored two great goals, he did very well defensively, winning duels and doing what he had to do", Guardiola added.
Real Madrid star Marco Asensio is not going to take part to tonight's Champions League clash between the Reds and Apoel.
Real will be bolstered for the visit of the Cypriot champions in midweek by the return of Cristiano Ronaldo.
In the last five matches, Apoel Nicosia has won three matches, lost one match and the other match ended in a draw.
"We try to protect the players we have".
"I hope that can help us to stop the talk of the hoodoo and everything".
"It's going to be hard, but we have a great team with great players and I think we can respond to all challenges this year", Modric recently told CNN Sport during Real's preseason tour of the US.