Why didn't the universe fall apart when Jesus died? In Colossians 1:16-17, it talks about how the world was made by Jesus and for Jesus. But it also says that "He is before all things, and in him all things hold together", so why didn't we all die and the universe, fall apart when Jesus died as it says that "in him all things hold together". Does this mean that Jesus's death wasn't fully death?

It's alright if you aren't a Protestant and you answer the question but it would be preferable to hear an answer from a Protestant.
I am answering the question from Evangelical Protestant perspective. 

The reason the universe didn't fall apart when Jesus died is that death does not mean "cessation of existence." 


  For as the body apart from the spirit is dead, so also faith apart
  from works is dead.
  
  James 2:26 (ESV)


James 2:26 says that death is a separation of body and spirit. Both do not undergo annihilation after death. Rather, both merely separated. 

Other Bible verses agree:


  . 2 I know a man in Christ who fourteen years ago was caught up to the
  third heaven—whether in the body or out of the body I do not know,
  God knows. 3 And I know that this man was caught up into
  paradise—whether in the body or out of the body I do not know, God
  knows— 
  
  2 Corinthians 12:2-3 (ESV)
  
  Yes, we are of good courage, and we would rather be away from the
  body and at home with the Lord
  
  2 Corinthians 5:8 (ESV)


This is perfectly attested in the death of Jesus Christ:


  Then Jesus, calling out with a loud voice, said, “Father, into your
  hands I commit my spirit!” And having said this he breathed his last.
  
  Luke 23:46 (ESV)


At Jesus' death, his spirit did not cease.Rather, he commited his spirit to his Father.


  Nicodemus also, who earlier had come to Jesus by night, came bringing
  a mixture of myrrh and aloes, about seventy-five pounds in weight.
  
  John 19:38 ( ESV)


On the other hand, Jesus' body was buried. 

Conclusion

Jesus, being God who became flesh, identifying with our limitation by his own choice (John 1:1,14; Phil. 2:6-7) to save us (Matthew 1:21) ,was not the only person who is fully God. The Father and the Holy Spirit, his co-equals do exist (Matthew 28:19) to take hold of the universe.Jesus is both God and Man ( Col. 2:9) and his death is 100% real. 

References:

http://www.gotquestions.org/absent-from-the-body.html

https://carm.org/soul-cease-exist-after-death