The Spaniard, who has lost his place as number one since joining the club for a world record fee for a goalkeeper in 2018, was introduced late in extra-time as a substitute for the shootout by Thomas Tuchel.
Kepa famously refused to be replaced by former Chelsea boss Maurizio Sarri in a League Cup final defeat to Manchester City two years ago. But this time he rewarded his manager's faith with saves from Aissa Mandi and Raul Albiol.
Chelsea's win over Manchester City in Porto to lift the Champions League for a second time in May was the culmination of a meteoric rise in Tuchel's first five months in charge. The German has bemoaned having to manage a 42-man squad during pre-season and could soon have even more firepower to call on with Romelu Lukaku expected to complete a return to Stamford Bridge later this week for a club record £97 million ($135 million).
But the depth of resources available to Tuchel was on show early on. Euro 2020 finalists Mason Mount, Ben Chilwell, Reece James and Jorginho all had to settle for a place on the bench after their late return to pre-season training, but Chelsea still had far too much for the Europa League winners in the opening half hour.
Bittersweet for Ziyech
Sergio Asenjo produced a brilliant reaction save to deny Timo Werner before N'Golo Kante fired just wide. Hakim Ziyech had a bittersweet evening as he continued his fine pre-season form into competitive action with the opening goal.
Marcos Alonso fed Kai Havertz down the right and from the German's low cross, Ziyech swept home. However, the Moroccan was forced off before half-time in a sling by a shoulder injury.
In stark contrast to Chelsea's haul of trophies in the nearly 20 years since Roman Abramovich's takeover transformed the club, Villarreal's Europa League final victory over Manchester United in May secured their first ever silverware.
After an overly cautious start from Unai Emery's men, going behind forced the Yellow Submarine out of their shell and they were unfortunate not to be level by half-time. Edouard Mendy scampered from his line to deny Boulaye Dia a debut goal.
Chelsea were still reeling for the loss of Ziyech when Alberto Moreno then smashed off the underside of the bar in first-half stoppage time. The woodwork came to Chelsea's rescue again early in the second-half, this time to deny Gerard Moreno.
Mendy's poor clearance fell straight to Dia, who played in the Spanish international, but Mendy made amends by tipping his effort on to the post. Villarreal were the dominant force after the break as Chelsea physically faded after their flying start.
Tuchel turned to his bench to stem the tide as Mount, Jorginho and Andreas Christensen were introduced. But the Spaniards finally got their deserved equaliser when Moreno played a clever one-two with Dia before firing high past Mendy.
Neither manager would have welcomed an extra 30 minutes just days before their respective league campaigns kick-off. Chelsea had the better of extra-time as Christian Pulisic fired inches wide before Asenjo produced another fine save to deny Mount.
Asenjo also gave Villarreal a dream start to the shootout by saving from Havertz. But Chelsea were flawless with their next six spot-kicks to allow Kepa to take centre stage.
Standout matches today