There are two issues with your code. First, when you are replacing the vowel in your second half, you are only doing it temporarily. You need to perform that operation in a separate line and save it in the second half variable.
Also, you are printing the your temporary result each time you go through the loop. If you only want it to only print once, just decrease the level of indent so that it is outside the loop. Here is how I would restructure it.
for char in secondHalf:
if char in vowels:
secondHalf = secondHalf.replace(char,(char.upper()))
newWord = firstHalf + secondHalf
print ("The new word is: ",newWord)