The match took place at Gelora Bung Karno Main Stadium, Jakarta, on Tuesday.
"Congratulations to the players, the coaching team, and officials for the first and crucial win for Indonesia towards the World Cup. I am proud of the hard work of the players," he noted in a PSSI statement.
Indonesia won Tuesday's match with two goals scored by Marselino Ferdinan in the 32nd and 57th minutes.
The victory catapulted the country into third spot in the preliminary standings of Group C with six points.
In the wake of Indonesia's 4-0 loss against Japan during a Group C qualifier match on Friday (November 15), Thohir issued an ultimatum, stating he would relinquish his position if the players and coaches failed to give their all for the 2026 World Cup qualifiers.
"After losing to Japan, I saw the players want to get back up, and that was shown in the match (on Tuesday). This is valuable capital for the next qualifier matches next year. Hopefully, we will be even more prepared," he stated.
The triumph marked a turning point for Indonesia, breaking a five-match winless streak that included three draws and two losses.
The Indonesian national team has played six out of 10 matches in the third round of the 2026 World Cup qualifiers.
In the four remaining matches to be played in 2025, Indonesia will face Australia on March 20, Bahrain on March 25, China on June 5, and Japan on June 10.