And their saying, 'We did kill the Messiah, Jesus, son of Mary, the Messenger of Allah;' whereas they slew him not, nor crucified him, but he was made to appear to them like one crucified; and those who differ therein are certainly in a state of doubt about it; they have no definite knowledge thereof, but only follow a conjecture; and they did not convert this conjecture into a certainty; On the contrary, Allah exalted him to Himself. And Allah is Mighty, Wise. (4:158-159)
The emphasis is upon their failure to murder Jesus by any means. The reader is reminded that the very beginning of the verse refers to the Jewish boast that they had succeeded in murdering Jesus.
This Jewish claim is firmly rejected by the Holy Quran. That is why by the end of verse, the conclusive declaration is that whatever may have happened they certainly failed to kill him. This implies that it is not the act of crucifixion which is denied. What is denied is death by crucifixion.