First, I'd like to propose two alternatives, if you and your partner are willing to put in a significant number of hours over the summer so that your son does not have to repeat the year: homeschool over the summer and have your child tested a week or two before the next school year starts to see if he's made enough advances to move ahead with his class, or summer school. More later.
How to make a 9 years-old son accept that he will repeat the school year?
You can't make him feel something he doesn't feel. It might be a wording issue, but to assume you can make someone feel differently about something is to invalidate the child's emotions, and through that, the child himself. If he feels desperate not to repeat the grade, you need to validate that, no matter how uncomfortable it is. So let him emote: cry, plead, be angry, mourn, whatever, for a while, and empathize with him. (You don't have to agree with him, but you do need to listen with empathy.) Tell him when he's ready, you would like to discuss some plans with him. If he says he'll never be ready, empathize with that, too, and explain that even when we are not ready to face something, it will still happen, so it's good to talk about it sooner rather than later, but ok, how about tomorrow?
When you talk, it might help both of you to draw up a list together on paper of all the "cons", his seemingly unimportant ones as well as the obvious. That way, he'll know you've heard all of his fears. When neither of you can think of any more, it will be time to start the "pros" (maybe after a break): he will not be generally behind his classmates, but instead be ahead in some things, even with them in others, and maybe behind in a few areas, but it will not be as difficult for him to master the material as it was this year. He will know what to expect as far as subjects and skills go. His teacher will be a good one (if you know this to be true.) That it may well make all of his schooling from this grade on easier. There may be kids in the class that he will like as friends. List every positive you can think of that is truthful. Thinking outside the box, the biggest pro I can think of is that this is an opportunity to teach resilience: that not every setback is a failure, that disappointments are also opportunities to learn, that moving ahead sometimes requires a change in direction, that long-term views are as important, or more so, than the immediate goals, etc. Some in-depth reading about it is important if parents are to give children the very valuable gift of resilience.
Once the lists are drawn up, ask your son to read the list of pros whenever he feels sad or worried about repeating the year. He may still feel sad, but maybe he can see the value in repeating the year, too.
While homeschooling may seem daunting, it really shouldn't be. When you subtract all the time taken up in class by waiting for others (getting their books out, getting in their places, quieting down, answering other kids' questions, etc., etc.), in the early elementary grades, you can cover everything in well under half the time it takes in class. Summerschool is offered in many places and may be an alternative for your son as well.
Want to learn more about grade retention? Read about it in the link.
Resilience guide for parents and teachers
Essential Questions Concerning Grade Retention