A penalty from Kai Havertz, who was the match-winner in last season's Champions League final, proved to be the decisive moment as he slotted past Weverton moments before the end of extra-time.
Romelu Lukaku's header broke the deadlock but Thomas Tuchel's men were pegged back shortly afterwards as Raphael Vega slotted home a penalty after the ball hit Thiago Silva's hand.
The match, which appeared destined for a penalty shootout, was lacking in clear-cut opportunities but Chelsea proved to be the more composed side in Abu Dhabi.
Their winner came as they were awarded a spot-kick when Cesar Azpilicueta's goalbound effort was blocked by Luan Garcia's hand.
And Havertz made no mistake as he sent the Weverton the wrong way to ensure Chelsea have now won every single trophy available to them.
Palmeiras' low block frustrated Chelsea time and again, but also the Stamford Bridge men were unable to find any real rhythm.
Callum Hudson-Odoi's deep cross evaded everyone in the box as a clutch of players tumbled over each other.
Azpilicueta rose to his feet to find himself in a fine position with Palmeiras keeper Weverton possibly stranded, but the Chelsea captain lost his bearings and the chance evaporated.
Palmeiras talent Dudu whipped over the bar after a smart spinning effort, then spurned a major chance by firing just wide after a quick break.
Mason Mount was then forced to trudge disconsolately out of the contest, in perhaps a recurrence of the leg issue that he had picked up in the 2-1 FA Cup win over Plymouth.
Chelsea's match-specific system demanded Thiago Silva act as playmaker, and his raking balls were often close to bisecting the Brazilians' defence.
A lack of movement and fluidity ahead though eventually led him to thump in a long-range effort that nearly caught Weverton cold.
The Palmeiras stopper pushed the ball around the post at full stretch, but Chelsea could make nothing happen from the resulting corner.
Chelsea's sparse fans only managed to make themselves heard for the first time in the opening moments of the second-half, such was the Palmeiras dominance in the stands.
The first time Chelsea broke in behind Palmeiras on the flank, the Blues took the lead.
Hudson-Odoi's first left-footed cross of the match proved a real peach and Lukaku's finish just as sweet.
The Blues expected to take control but were quickly pegged back instead, as the previously-flawless Silva was punished for a handball in the area.
Silva handled when battling with Gustavo Gomez for a clearing header, and the penalty was awarded after a VAR check.
Veiga showed no nerves when rifling the spot-kick home, sending Mendy the wrong way.
Neither side could force any further breakthrough in an edgy end to normal time, and so an extra 30 minutes rolled around.
Chelsea set about trying to win the title without any need for penalties and Pulisic almost forced a second Blues goal.
The USA forward's cut-back was deflected goalwards, only to loop onto the bar and bounce to safety for the relieved Palmeiras defence.
Just when the tie looked headed for a shoot-out however, Chelsea won an extra-time spot-kick instead.
Luan was penalised for blocking a shot with his hand after another VAR review and Havertz kept his cool to fire home in style.
Luan was then sent off to add insult to his personal injury, but the Blues deserved their win in the end, and the chance to complete their trophy cabinet.