The South Korean attacker netted in the ninth and 16th minutes at BayArena to give Leverkusen an early two-goal lead against his former club.
Hamburg managed to respond with two of their own through Maximilian Beister and Pierre-Michel Lasogga by the 49th minute mark of the contest before Son completed his hat-trick ten minutes into the second half.
The 21-year old then set up Stefan Kiesling for Bayer's fourth prior to Lasogga giving Hamburg hope but in the end the home side were able to record a victory with Gonzalo Castro adding a fifth in the final minute of regular time.
The victory allowed Leverkusen to remain third on the table and also saw Son score his first treble of goals in Germany's top flight but it prompted mixed emotions from the Asian ace who contributed to the demise of Hamburg but also playing a part in their third goal.
"We haven't managed to score that many goals in a single game so far this season. I'm delighted with the win," he told the Bundesliga's official website.
"However, I'm still annoyed with the mistake I made in the lead-up to their third goal. I was really upset about that, but fortunately we were then able to score the deciding goal on the counter to make it 5-3.
" it also makes me feel a little hurt and sad because HSV are my former club. Of course though, it was the game in which I scored my first Bundesliga hat-trick, but I can still enjoy it a little bit."
Son added: "It definitely gave me goosebumps because the fans were chanting my name. I'm really happy about that right now because I've never experienced anything like that in my career."
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball