The Real Madrid star was depicted lying on train tracks in an advertising campaign in Sweden prior to the World Cup playoff clash, prompting uproar from Portugal.
The company ran a number of adverts ahead of the second leg of the World Cup qualification playoff between the nations on Tuesday, with the Real Madrid star depicted as a small doll lying on train tracks with the caption 'We're going to pass over Portugal'.
Another image shows the model of the 28-year-old with dozens of pins stuck in.
The advert led to uproar among Portuguese nationals, with a Facebook group set up urging those angered to boycott the brand, prompting Pepsi to offer its apologies for the campaign.
"We would never want to put the sport or the spirit of competition in a negative light," an official Pepsi statement reads.
"We regret it if people were offended by the posts. They were immediately taken down. We would like to extend our apologies to all concerned."
Ronaldo would eventually go on to lead Portugal to the World Cup as he netted a hat trick to help the Seleccao to a 3-2 away-win after previously scoring the winner in the first leg.
CAN YOU BELIEVE IT? | Ronaldo's head trapped beneath a crushed Pepsi can
PINNED DOWN | The Real Madrid star covered with dozens of needles
POOR TASTE | The prolific attacker as a voodoo doll tied to railway lines