The 31-year-old led City to a 1-0 victory over his former club Orlando Pirates at Cape Town Stadium on Saturday.
Johannes, who will join Bidvest Wits in the new season, was pleased to register a win in front of friends and family, but admits the occasion was also tinged with sadness.
"Firstly, I was just fully focused on getting three points for the team as we needed that you know," Johannes tells KickOff.com.
"I also need to admit that after that I was very emotional as all my friends are family were there to support me - that was a very special feeling.
"At the same time it made me realise that I won't have the privilege and honour of playing regularly in front of them. We must remember our friends and family are the ones that root for us with every home game. It's for the fans that one raises your game. They spend money to watch us and expect quality and value.
"Therefore, I'll miss the interaction with the City crowd and off course my family and friends. I feel honoured to join a club like Wits but at the same time I will miss the love and warmth here in Cape Town. I have to admit apart from winning the treble with Pirates and a few trophies with Sundowns, my two seasons at City here in my hometown has been the most amazing of my career and I will always be grateful.
"Friends I met here became family, you know. If I think of the fantastic players I played with here at City... players like Lebo [Manyama], Aubrey [Ngoma], 'Major' [Lehlohonolo Majoro] and this season we have players like Teko [Modise].
"It's a like a bitter-sweet moment but I have to look ahead as I'm also very excited to join a top class coach like Gavin Hunt and his team."
Johannes, who has endured his fair share of highs and lows in his career, went on to reveal a bit of helpful advice he received as a teenager from an official at University of Pretoria.
"I will never forget what he said to me when I was 17 years old after I joined Mamelodi Sundowns... 'It's not how many games you play but how many seasons'. And that just stuck with me.
"But look, I'm very fortunate to have such a long career. I have been blessed especially not having major or serious injuries in the last four to five seasons.
"Thanks to all the people at the club from the office staff to the backroom staff. Lastly to my coach [Benni McCarthy], you are one in a million and thanks for allowing me to grow my game more under you," Johannes concludes.
The fifth-placed Citizens will end 2017/18 against AmaZulu at King Zwelithini Stadium in Umlazi, Durban on May 12.