Berrettini, who needed a medical time out for what appeared to be hip pain after three games in the second set, threw in the towel at the change of ends after being encouraged to do so by his entourage.
World number 104 Arnaldi, who spent 17 hours and 42 minutes on court as he fought his way into the last eight, will face compatriot Flavio Cobolli on Friday, guaranteeing an Italian presence in Sunday's final despite the early exit of world number one and last year's runner-up Jannik Sinner.
Arnaldi, who had played over 10 hours in the two previous rounds, spent two hours on court Philippe Chatrier on Wednesday.
"It's a tough one. We both played a lot so it's normal to not be at our best but you never wish someone's tournament to end like this," Arnaldi said.
"We're doing such a good job in Italy. I hope he recovers, the grass season starts soon and he's someone who is going to be tough to play against.
"I'm tired, that's for sure, but I train and play tennis and to play these tournaments, these matches. I try to give it all I've got. I was more tired than usual and wasn't as fast as I think in the first match. I was injured not long ago but I'm giving all I have now."
