Martins scored the only goal in the first leg 1-0 win for Shanghai Shenhua last weekend.
Wenjun Lue gave Shanghai SIPG the lead in the 16th minute on Sunday before Yunding Cao drew Shanghai Shenhua level on the stroke of half-time.
Martins scored to make it 2-1 to Shanghai Shenhua in the 68th minute but Brazilian forward Hulk made it 2-2 after converting a 72nd minute penalty.
An own goal by Giovanni Andres Moreno in the 76th minute gave Shanghai SIPG a 3-2 lead.
In the 90th minute, Shanghai SIPG were reduced to 10 men following Huan Fu’s sending off.
Shanghai Shenhua have now won their first Chinese FA Cup title since 1998 and have now won it for the fourth time.