Python 2, 84 74 bytes

i=input();o=""
for x in"kMGT ":o=(i,x+i[-3:])[len(i)>3]+o;i=i[:-3]
print o

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Previous version for 84 bytes

i=input()[::-1];o=""
for x in"kMGT ":o+=(i,i[0:3]+x)[len(i)>3];i=i[3:]
print o[::-1]

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• Reverse the input
• Step through backwards in threes appending prepending the next letter
• Reverse and print

Not sure that this is the most efficient approach but it's the best I can come up with at the moment.