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We know he was substituted as it does say in the Holy and Noble Qu'ran:

...They said, “We killed the Messiah Jesus, son of Mary, the messenger of God." They did not kill him, nor did they crucify him, but the likeness of him was put on another man (and they killed that man)... (Qur'an, 4:157) Ibn Abbas said:
"Just before Allah raised Jesus to the Heavens, Jesus went to his disciples, who were twelve inside the house. When he arrived, his hair was dripping with water (as if he had just had a bath) and he said, 'There are those among you who will disbelieve in me twelve times after you had believed in me.' He then asked, 'Who among you will volunteer for his appearance to be transformed into mine, and be killed in my place. Whoever volunteers for that, he will be with me (in Paradise).' One of the youngest ones among them volunteered, but Jesus asked him to sit down. Jesus asked again for a volunteer, and the same young man volunteered and Jesus asked him to sit down again. Then the young man volunteered a third time and Jesus said, 'You will be that man,' and the resemblance of Jesus was cast over that man while Jesus ascended to Heaven from a hole in the roof of the house. When the Jews came looking for Jesus, they found that young man and crucified him. Some of Jesus' followers disbelieved in him twelve times after they had believed in him. They then divided into three groups. One group, the Jacobites, said, 'Allah remained with us as long as He willed and then ascended to Heaven.' Another group, the Nestorians, said, 'The son of Allah was with us as long as he willed and Allah took him to Heaven.' Another group, the Muslims, said, 'The servant and Messenger of Allah remained with us as long as Allah willed, and Allah then took him to Him.' The two disbelieving groups cooperated against the Muslim group and they killed them. Ever since that happened, Islam was then veiled until Allah sent Muhammad."
—Al-Nasa'i, Al-Kubra, 6:489 I personally believe that when Isa asked Allah to have the cup pass over him and Allah heard his prayers and spared his life However as a punishment for betraying Allah's prophet, Judas was made to look like Jesus. And so Judas suffered and was crucified. And this is a possibility for the fact that there is no solid record on how Judas died. The Bible gives two stories. 1) He killed himself. 2) He bought land and when he went unto his land he fell and died.