There was better news for Thiem, a finalist in Barcelona a year ago, who saved set point in the opener en route to a 7-6 (10-8) 6-1 victory over Spanish wildcard Jaume Munar.
World No. 1 Nadal, who also had a bye to the second round, packed out the main court at the Real Club de Tenis in Barcelona which is named after him.
"I've had a very hard time in the last 12 months with the injury and everything else that's happened", Djokovic said after his first match win in Monte Carlo.
"I made a great first set although I was a bit clueless when I got 4-0 in the second set, the rival gained confidence and began to play more aggressive". He lost just 21 games on the way to his 11 title at the Principality and has now switched his attention to the Barcelona Open, where he has progressed to the last 16.
"I felt pain in three different parts of my body while warming up, and wasn't able to perform to my best", he said.
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After a strong start at the Monte Carlo Masters in his last event, Djokovic lost to Dominic Thiem in the third round.
Ten-times tournament victor Rafael Nadal was in action against fellow Spaniard Garcia-Lopez later on Thursday. He has won 32 of his last 33 matches on the surface, including 15 straight.
Nadal consequently extended the record for most consecutive sets won on clay to 38, and will next meet Guillermo Garcia-Lopez, who went through after Nishikori withdrew.
Nadal needs to win his 11th Barcelona title this week to retain his No. 1 ranking.
Second seed Grigor Dimitrov of Bulgaria also slipped past Frenchman Gilles Simon 6-2 6-1 to reach the last 16.