The 20-time grand-slam victor took on Kyrgios as the centrepiece of Wednesday night's event and prevailed 7-6 (8-6).
Stars including Rafael Nadal, Serena Williams, Novak Djokovic, Caroline Wozniacki, Stefanos Tsitsipas and Alexander Zverev also played Fast Four doubles at the event that helped raise an incredible $4,826,014.
Tennis greats Roger Federer of Switzerland and Rafael Nadal of Spain pledged to donate 250,000 Australian dollars (172,000 USA dollars) towards the Australian bushfire relief efforts at a charity event on Wednesday in the lead-up to the Australian Open.
We are very excited to announce that the world's best players will be at the AO Rally for Relief.
Tournament organisers have been under fire for ploughing ahead with the qualifiers after an initial delay on Tuesday, with players complaining of breathing difficulties and one forced to retire from a match after suffering a coughing fit.
I had a great season previous year and a lot of fun playing tennis; I like to compete and that's why I'm not afraid of losing because I'm a target now. "I wanted to go out there and play, even though I've got a four centimetre, grade two tear, so it's not a joke, it's something really serious", he said. "It was emotional", Kyrgios, an Australian native, said.
But Djokovic said the challenge wouldn't just come from the established order, and revealed that he wouldn't be surprised if one of the up-and-coming stars of the game breaks through to win a big tournament soon.
At least 28 people have died so far in the wildfires throughout the country, and more than 3,000 homes have been destroyed or damaged in New South Wales alone, according to CNN.
Australian Nick Kyrgios has pledged A$200 for every ace he hits this month.
"I'm aware that at 38 I shouldn't be the favourite, it should be someone probably in their 20s, but the three of us have been able to stay as the favourites which is great for us", Federer said.
Smoke from the fires has caused disruption to the Australian Open qualifying and prompted criticism from some players about the conditions.
The ATP on Sunday pledged $500,000 to the WWF Australian Wildlife and Nature Recovery Fund as part of the bushfire relief efforts.