The match at the Darulmakmur Stadium, Kuantan on Saturday (Oct 27) night ended 3-3 in regulation time, which sent the tie into extra time.
Kedah, the FA Cup champions, got their goals through Fernando Rodriguez (eighth and 118th minutes), Jonathan Bauman (54th), Baddrol Bakthiar (85th) and Renan Alves (93rd).
Pahang's goals were scored by Dickson Nwakaeme (33rd and 121st) and Lazarus Kaimbi's brace (72nd and 75th) and Herold Goulon (penalty, 114th).
The first leg of the semi-finals at the Darulaman Stadium in Alor Setar last week ended in a 3-3 draw.
With the result, the Red Eagles edged Pahang on the away goal rules and will meet Super League champions Johor Darul Ta'zim in the Malaysia Cup Final.
The Malaysia Cup final will be held at the National Stadium in Bukit Jalil on Nov 2.