Federer broke Wawrinka's serve three times in the first seven games of the all-Swiss final, setting the tone for a 6-1, 6-3 win.
Federer collected his second title at the eight-man exhibition tournament.
He won the Kooyong title in 2005, the year he lost in the Australian Open semifinals to eventual champion Marat Safin.
Federer is one win away from equaling Pete Sampras' record 14 Grand Slam singles titles. With the Australian Open starting Monday, he didn't want to waste a minute of preparation time for the season's first major.
Federer and his Davis Cup teammate frequently hit together and the No. 2-ranked Federer considers himself a mentor and "like a brother'' to Wawrinka.
At Kooyong, he taught 23-year-old Wawrinka that he doesn't believe in friendly matches, even at exhibition tournaments.
"It's nice to play him. We played next to each other. Now he's on the other side,'' he said. "I wanted to see how much he's improved.''
The second-ranked Federer was entered but withdrew from the Kooyong tournament last year while struggling with mononucleosis.
He went into the Australian Open without proper preparation and was beaten in the semifinals by eventual champion Novak Djokovic, ending his streak of 19 straight match wins at Melbourne Park. He is 31-2 since the 2004 Australian Open, which was the second of his 13 major titles.
Federer has a tough draw at the season's first Grand Slam event, opening against Andreas Seppi of Italy, then possible matches against former No. 1 Carlos Moya in the second round, Safin in the third and Wawrinka in the fourth. Another semifinal against Djokovic looms.
Rafael Nadal, who ended Federer's 237-week streak at No. 1 last season after beating him in the French Open and Wimbledon finals and winning the Olympic singles title at Beijing, is on the other side of the draw, along with Britain's Andy Murray.
In the third-place match at Kooyong, Spaniard Fernando Verdasco had a 6-4, 6-3 win over second-seeded Fernando Gonzalez of Chile.
Gonzalez has one of the toughest opening-round matches at the Australian Open, which starts Monday, facing local favorite and former top-ranked Lleyton Hewitt.
Federer wins Aust. Open tuneup event at Kooyong
Getafe’s Manu Del Moral Only Out For Ten Days
