"I feel a little bit unusual".
That was as good as it got for the 22-year-old.
It was Djokovic's first match since splitting with longtime coach Marian Vajda.
"I think if he continues playing as he's been playing today and winning matches, it'slogical we're going to see the same Djokovic as we're used to seeing". "Eventually the game will come together".
Nadal broke his opponent's serve for the first time in the third game of the second set, before saving four break points in the fourth to move into a comfortable lead.
Goffin put up a spirited fight against the Spaniard until the tie-break, which was dominated by Nadal who converted his second set point.
The Briton, who was thrashed by the Croatian by an even wider margin in the Dubai Championships in 2015, performed poorly in the first set, losing three service games and looking increasingly frustrated.
He was forced to play down suggestions that former world number one Andre Agassi is in line to assist Djokovic on a full-time basis ahead of the French Open.
It was Dimitrov who struck first again in the second set, but this time Thiem was able to turn the advantage his way, breaking back and then once more to take the lead, serving out the second set with a lot more ease.More news: Jimmy Carter urges Trump to push for peace
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Play starts for the Madrid Masters quarter-finals at 12pm (11am BST).
However, Nadal conceded that the match will be tough and he has to be at his very best against the world number two.
However, the 14-time Grand Slam champion has a hard route to that potential matchup as he faces Fabio Fognini later Wednesday and potentially Nick Kyrgios in the third round.
Kyrgios did what his compatriot Bernard Tomic on Tuesday could not - down American Ryan Harrison.
David Goffin awaits the victor of Nadal's clash with Australian Kyrgios as the Belgian beat world number six Milos Raonic 6-4, 6-2.
Nick Kyrgios plays a forehand back to Rafael Nadal.
Number three seed, Simona Halep is into the quarter-finals after her 6-4, 4-6, 6-4 victory over 16 seed Samantha Stosur and she will be joined there by Rumanian wild-card, Sorana Cirstea and Kiki Bertens.
The German's earlier Madrid results, however, were enough to ensure that she will return to the top of the rankings next Monday, displacing Serena Williams.
A finalist in Madrid in 2014, Nishikori lost his last 10 matches against Djokovic, including in the semifinals in Madrid previous year.
"Novak is someone that I don't have good record (against)", Nishikori said. I will check it, I hope it's not too serious.