Cristiano Ronaldo converted the spot-kick to win the tie 4-3 on aggregate for the Spanish side.
"Let's be clear about one thing first: Michael Oliver got the two important decisions at the end of last night's game absolutely spot on," Clattenburg wrote in his column for The Times.
"Medhi Benatia's challenge on Lucas Vazquez was a penalty. Michael will have seen from his view what was a small push by Benatia...
"From his angle, the assistant referee would have seen the foot wrapping around Vazquez's body... It's a clumsy foul, but it's still a foul."
Oliver was also criticised for sending off veteran Juventus goalkeeper Gianluigi Buffon for heatedly protesting the penalty, a move which led the Italy international to blast the referee after the match.
Clattenburg said Oliver's decision was the right one as Buffon furiously confronted the referee twice.
"There was clear dissent from Buffon and what probably made Michael's mind up to send him off was that Buffon confronted him twice...," Clattenburg, who is the head of refereeing for the Saudi Arabian Football Federation, added.
"What he (Buffon) said is almost less important than the manner in which he said it..."
Clattenburg also pointed to the pressure on Oliver, who officiated in the Merseyside derby in the Premier League last weekend before the Champions League game and will also oversee Monday's match between West Ham United and Stoke City.
The 43-year-old Clattenburg believes the immense pressure is leading top-flight referees to quit sooner.
"Michael is the best referee in the Premier League...," Clattenburg said.
"The reaction to Wednesday will be a test for him, even though he can watch the game back and see he did well... There is no reason why Michael will not referee finals in the next few years.
"But there is a problem that the pressures of refereeing are making careers at the top level shorter. This applies to other countries in Europe as well."
(Reporting by Aditi Prakash in Bengaluru; editing by Sudipto Ganguly)
