Having been due to play the fourth-round match on Monday, Djokovic and Bautista Agut eventually took to the court just after midday on Tuesday.
In two bursts they were able to play for a minute over two hours, despite drizzle falling virtually throughout, and Djokovic led 4-1 in the third when finally the day was abandoned.
More leaden skies greeted the players on Wednesday, but it was at least fairly dry and Djokovic eventually ground out a 3-6 6-4 6-1 7-5 victory.
The Serbian appeared to let the conditions get to him in the first set on Tuesday, but, although never finding his best form, he was mentally tuned in thereafter.
Simona Halep and Agnieszka Radwanska were both furious at having been made to play in the rain after losing their fourth-round matches.
Djokovic said: “I remember early in my career I played a match against ( Nicolas) Kiefer at Wimbledon for five days. This is probably the second longest.
“Conditions were definitely on the edge throughout the entire day (on Tuesday). Bautista and I played I think more than two sets
in the mist. It was literally maybe five to 10 minutes of the entire stay of over one-and-a-half hours we had on the court without rain.
“But, once you accept the circumstances and the decision is such that you play, then you have to go with it.
“It was a great mental test for all of us. I’m in a way glad to have a match like this, because it’s a challenge that you need to overcome.
“The priority should always be the health of the players, no doubt. So I understand the frustrations that some players are going through.”
Ballkids are getting all the love! ICYMI: @DjokerNole celebrates match point w/ the help of this fella. #RG16 https://t.co/fwED2thfSN
— Roland Garros (@rolandgarros) June 1, 2016
As well as the players, some fans were also unhappy that, because those on Chatrier saw a minute over two hours of play, they are not entitled to any refund, while supporters on other courts will receive 50 per cent.
Bautista Agut fuelled conspiracy theories by saying: “I can understand the view of the tournament. They pushed us to play two hours.”
But tournament director Guy Forget, who is in his debut year in the job, insisted all decisions were taken “with the best of intentions”.
He said: “We, the tournament organisers, have been harshly criticised over the past few hours. The way we handled the situation, while we acted with the best of intentions, has been questioned. I would like to provide some clarification.
“The decision to suspend or resume play lies solely with tournament referee Stefan Fransson. Respect for the game always takes precedence.
“If what we are being accused of were true, it would have been in our best interests as organisers to stop play before the one-hour 59-minute mark as our insurer would have been responsible for ticket reimbursement.
And the world No1 is through to his 10th QF here (36th at a Major) w/ 3-6 6-4 6-1 7-5 win over Bautista Agut. #RG16 pic.twitter.com/fXUuXVXnrh
— Roland Garros (@rolandgarros) June 1, 2016
“However, that was not the basis of our decision. Our aim was to play for as long as possible, even if that meant being criticised for playing in difficult conditions.
“I understand that not refunding spectators with tickets to the Philippe Chatrier Court has caused frustration and anger. But can we really change the rules in the middle of the game?”
Djokovic, who becomes the first player to win 100million US dollars in prize money, now faces having to play five times in six days, starting with a quarter-final against Tomas Berdych on Thursday.
.@DjokerNole is the sport's first US$100 million man - passes prize money milestone at #RG16 https://t.co/hHPQhhnyRa pic.twitter.com/TSn1aYqMuC
— ATP World Tour (@ATPWorldTour) June 1, 2016
