Federer, one away from equaling Pete Sampras' record 14 Grand Slam titles, broke Wawrinka's serve three times in the first seven games to win the all-Swiss final 6-1, 6-3.
His said he wants to use every chance to build momentum for the season, and put his friendship aside for 57 minutes against Wawrinka.
Federer also won the Kooyong exhibition tournament in 2005, the year he lost in the Australian Open semifinals to eventual champion Marat Safin.
With the Australian Open starting Monday, he didn't want to waste a minute of preparation time.
"New season, big opportunities for me,'' Federer said. "I'm chasing a lot of records.''
Federer had three wins in the eight-man draw this week and said he saved his best for last, ripping some trademark backhand winners down the line and rarely letting Wawrinka get into the points.
"Sorry Stan!'' he said. "It's a wonderful preparation for the Australian Open. I'm excited.
"It was serious, not crazy serious. We have to be tough against each other, but we played some great tennis.''
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. They combined to win the Olympic doubles final in Beijing last August.
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 was beaten in the semifinals of the Australian Open 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.
"This time is different. I've Played plenty of matches. Also played Doha,'' he said. "Last year was just a matter of playing the tournament. This time I'm trying to win it.''
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.
When the possible fourth-round match up was mentioned Saturday, Federer and Wawrinka, sitting side-by-side at the trophy presentation, looked at each other, smiled and nodded.
Rafael Nadal, who ended Federer's 237-week streak at No. 1 last season after beating him in the French Open and Wimbledon finals, 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.
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