Ferrer said the match was one of his best ever at the season-opening Grand Slam, yet the Spaniard was still racked with doubt that he could go on to win the title next week.
Baseline hustler Ferrer worked his Japanese opponent around the court, waiting for the 23-year-old to make one of his 65 errors. Although the Japanese number one made it difficult, the fourth seed closed out a 6-2 6-1 6-4 victory.
"I played very good, one of the best matches on my career in Australian Open," said Ferrer. "Nishikori is a very great player. I think he's going to be top-10.
"He has everything ... (and) the result, it was in three sets, but the game, it was very, very difficult."
Ferrer entered the tournament having won a record-equalling fourth Auckland title, and will officially supplant injured compatriot Rafael Nadal as the world number four by the conclusion of the Australian Open.
The 30-year-old, however, did not consider himself in the same league as the 'Big Four' of Novak Djokovic, Roger Federer, Andy Murray and Nadal.
"No, no, I think the top four, they are better," Ferrer said when asked if he felt he belonged in the echelon of players at the top of the men's game.
"It is very difficult to win a Grand Slam because there are the top four. In this moment, the last three or four years, they are better than the other players.
"I am top four because Rafael is injured a long time."
Ferrer's self doubt is based on a sound reasoning, which he also acknowledged after his victory on Sunday.
Until 2012, his best season on the Tour with seven titles, he had reached the quarter-finals or better at a Grand Slam only five times since 2003. His best run at Melbourne Park was to the semi-finals in 2011.
"I am not thinking about if I have the chance to win a Grand Slam," he said of his mentality given his propensity to crash out earlier than expected.
"When the player arrives in the second week it is because he is playing good and we are confident with our game.
"(So) I am only focus (on) every match I will play."
Many observers have also said while he is one of the fittest and best returners and retrievers on the ATP Tour, he lacks the killer shot the other top players have,
The Paris Masters champion also said he was still unsure if he had the arsenal to beat Djokovic, Federer or Murray to take his first Grand Slam.
"It's my opinion, okay," he said when asked why he did not seem to have the self belief to break through.
"I am trying to improve my game. I am trying to improve my serve. I am trying to play more aggressive with my shots. But it is difficult for me now improve too much my game.
"But I am trying to do my best every match. I am trying to win every match anyway, top four, top 10, or top hundred."
Ferrer will next play fellow Spaniard Nicolas Almagro after the latter's fourth-round opponent Janko Tipsarevic retired hurt in their match.
Eighth-seeded Serb Tipsarevic received treatment on a foot injury and pulled the pin when trailing 6-2 5-1 in the match at Hisense Arena.
The 10th-seeded Almagro advances to his first quarter-final at Melbourne Park in his ninth appearance at the year's first Grand Slam after making the last eight at the French Open three times.
Tipsarevic had played two successive five-set matches coming into the Almagro clash and said in the lead-up that his legs were going to "feel" it.