After helping Spain qualify for the Davis Cup semifinal, Nadal revealed he arrived in Monte Carlo in good condition but conscious that injuries might flare up again.
Rublev spurned a chance to seal the match when he fired a forehand narrowly wide on his own serve late in the deciding set. "I'm obviously lacking that match play".
Grigor Dimitrov and Dominic Thiem beat Pierre-Hugues Herbert and Andrey Rublev respectively to advance to the third round of the Monte Carlo Masters.
"I could have won the match earlier definitely, but it was great to deal with these kinds of emotions again", the 12-time Grand Slam champion said.
Djokovic - seeded ninth at an event he has twice won - will face Austria's fifth seed Dominic Thiem on Thursday for a quarter-final place.
"It's a terrible draw for sure, from the first round on", conceded Thiem.
Though it was a one-sided first set score, it still lasted the best part of 40 minutes as Nadal wore down his opponent.
"He is very motivated to do well and I am looking forward to playing against other top players".
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Nishikori returned from injury in February, after a torn tendon in his right wrist ruled him out of last year's U.S. Open and this year's Australian Open. With five consecutive points, Djokovic came to a new break. "All I (could) do was just fight and win".
Also advancing was former World No.6 but unseeded in this tournament, Kei Nishikori.
The 20-year-old Zverev had appeared in control of the first set when he broke for a 4-3 lead. I feel like Tomas was struggling a little bit in second, and third too.
Earlier, French number one Lucas Pouille blew a one-set lead to be dumped out by Zverev's older brother Mischa in a third-set tie-break.
Thiem made the most of the reprieve, breaking him with backhand pass down the line and holding for 6-5.
Fabio Fognini (ITA) bt Ilya Ivashka (BLR) 6-4, 7-5.
The Belgian sixth seed, who lost to Nadal in last year's semi-finals, sealed victory on his fourth match point. Muller saved the first match point with a strong serve but lost to the imposing German on the next with a double fault.