The existing 5,100-strong task force will be incorporated into a broader international mission, he announced.
French forces have been operating in Mali, Chad, Mauritania, Niger, and Burkina Faso to fight militants.
Last week, France paused operations in Mali following a military coup.
Militants linked to al Qaeda and the Islamic State (IS) group have strengthened their grip on the region, which has become a front line in the war against Islamist extremism.
It is also a major transit route for illegal drugs, weapons and jihadists.
"We will keep a counter-terrorism pillar with special forces with several hundred forces... and there will be a second pillar that will be co-operation, and which we will reinforce," Mr Macron said during a press conference on Thursday.
The president said the drawdown of troops would take place in an "organised way".
"France has been involved for a little over eight years in the Sahel," Mr Macron said. "Many of our soldiers have fallen. I think of their families. We owe them consistency, clarity. We're going to learn from what worked and also learn from what didn't."
In recent months Chad's leader Idriss Déby Itno was killed in battle and Mali experienced its second coup in nine months.
Following the second Mali coup, Mr Macron told a French newspaper that he had told regional leaders that France would not support countries where there was no democratic legitimacy or transition, and that France had no intention of keeping its troops in Africa forever.