A week after winning the TotalEnergies Africa Cup of Nations, goalkeeper Edouard Mendy got to keep goal for the Blues and Romelu Lukaku partnered Kai Havertz.
It was the Blues that had a tough start earlier on when Dudu made a surging run down the wing after he escaped three challengers before going over the top from the cusp of the area.
Chelsea were requested to put on a substitution after the half-hour mark where an injury forced Mason Mount to cut his evening short and Christian Pulisic entered.
The make-up didn't unsettle the Blues as a chance to veteran defender Thiago Silva followed on the stroke of halftime, but this attempt was courted by Weverton.
After a strong finish to the first half, the European champions hit the front nine minutes into the restart when Lukaku dropped off Luan Teixeira to head in a ball from Callum Hudson-Odoi.
Palmeiras struggled to contain the Blues minutes thereafter and brought Danilo to a chance from a promising area on the edge of the box, but Weverton witnessed the shot go wide.
However, the South American champions were given a route back with Silva flagged for handling in the area in addition to conceding a penalty-kick, which Raphael Veiga converted.
With chances presented particularly for Lukaku as the clock ticked away, the forward wasn't able to profit and allowed the match to go to extra-time.
Chelsea should've gone back ahead from a reverse pass by Pulisic on 99 minutes after he combined with Timo Werner, but his attempt were deflected onto the woodwork.
The Blues eventually regained their lead after an 18 minute spell when Havertz netted from the spot with Luan deemed to have handled Cesar Azpilicueta's shot.
Palmeiras went in desperate search for the equaliser with time running out and finished with ten players after Luan got a red card for a rough challenge on Havertz, as the Blues held on for the win.