Djokovic overcame a stern examination from Marin Cilic to prevail 4-6 6-2 6-3, while Federer stayed on course for his first title in the French capital since 2011 with a 6-4 6-4 victory over Kei Nishikori.
"I won the match, but if he would've won it, it would've been absolutely deserved".
"I'm in the semifinals of a Masters 1000 only for the fourth time", Thiem said.
That streak includes a Cincinnati Masters final win against Federer.
Chasing his 100th career title after winning the Swiss Indoors last Sunday, the 20-time Grand Slam champion was hardly troubled.
This time he went right to left with a forehand volley that infuriated Nishikori, who shaped to belt the ball down the court as a ball boy went to catch it, and two points later Federer had secured the set.
The Japanese consequently appeared to lose all composure, gifting Federer another break at the start of the second.
Should Federer find a way to get past Djokovic then beat the victor of the other semifinal-between two of tennis' best young players in Karen Khachanov and Dominic Thiem-he would join Jimmy Connors (109) as the only player with triple-digit ATP singles titles.
Djokovic, who will return to world No.1 next week, had his personal best winning sequence of 30 consecutive sets ended as Cilic played nearly flawlessly aggressive tennis to draw first blood in a magnificent duel.
So intense was the Serb that even when he was fighting back in the second set, leading 5-2, he ended up screaming at his team at the top of his voice, demanding to know why he had not received the vitamin tablets he had been asking for.
Djokovic broke his racket in frustration and then broke Cilic straight back, after which the momentum shifted back in his favor as Cilic lost to him for the 16th time in 18 meetings.
It was in Cincinnati that Federer and Djokovic last met with the 37-year-old winless against his "Big Four" rival since 2015. It's kind of a flu.
Djokovic had his personal best winning sequence of 30 consecutive sets ended as Cilic played nearly flawlessly aggressive tennis to draw first blood in a magnificent duel.
It was also Djokovic's 21st consecutive win since losing to Stefanos Tsitsipas in the third round of the Rogers Cup in August.
Khachanov, 22, shrugged off complaints from Zverev over noise coming from the Russian player's box during the match. And they also then started changing the string back in 2002 with the switch of the head size, because I was just shanking the balls too much, especially on windy days, and because I was brushing the ball that much.
The day's action in Paris ensured that Cilic and Thiem are now guaranteed the last two of eight places on offer for the ATP Finals in London this month.