It is important to refer to the proper context of this verse. The Jews were plotting a scheme against Jesus PBUH, i.e, they wanted to arrest and crucify him. Whereas, God’s scheme, referred to in 3:54 was to counter this and shield Jesus from their plotting. So what was God’s scheme? It is mentioned in the next verse:
3:55 God said, “O Jesus, I will terminate you, and raise you to Me, and cleanse you of those who have rejected, and make those who have followed you above those who rejected, until the day of Resurrection; then to Me is your return so I will judge between all of you in what you were disputing.”
Clearly, God outwitted the scheme of Jews and their intention of throwing Jesus to oblivion miserably failed. Conversely, it helped to trigger a revolution and Jesus’s message was soon to spread far and wide. Not only were the Jews subjected to a severe punishment in just a few years after rejecting Jesus PBUH (devastated at the hands of Romans), but God has ordained that the followers of Jesus PBUH will hold supremacy over Jews for all times to come. It was this scheme of God by which he exonerated, defended and honored Jesus against Jews, which is referred to in 3:54. This supremacy of followers of Christ over Jews is self-evident in terms of influence, worldly power and numbers.