Cesar Azpilicueta missed and Mason Mount saw his spot kick saved for Chelsea as Kostas Tsimikas scored the crucial penalty.
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The sides, meeting in a second domestic cup final this season, played out an entertaining goalless draw over 120 minutes before being decided on penalties again.
Liverpool were on top in the early stages with Luis Diaz a particular threat. A through-ball from Trent Alexander-Arnold put Diaz through on goal in the eighth minute but Edouard Mendy denied him before Naby Keita put the rebound wide.
Chelsea responded well to Liverpool’s pressure with Christian Pulisic going close on 23 minutes after excellent play between Mount and Reece James on the right wing.
Shortly after, Pulisic’s pass gave Marcos Alonso a sight of goal but Alisson was off his line quickly to deny the Chelsea defender.
On 33 minutes Liverpool suffered a blow when Mohamed Salah was forced off through injury. Diogo Jota came on in his place and put a good chance just over moments before half-time.
Chelsea made the faster start after the break with Pulisic drawing a save from Alisson and Alonso striking the crossbar from a free kick but both sides toiled and could only create half-chances for much of the second period.
However, Liverpool had a golden chance to win the game when substitute James Milner’s cross found Andy Robertson but he struck the post from close-range.
Liverpool were dealt another blow ahead of extra-time as Virgil van Dijk went off, seemingly injured, and was replaced by Joel Matip.
Neither side were able to find a breakthrough in the additional 30 minutes, meaning spot kicks for the second time this season.