Federer arrived at the $3.65 million season-ending event with only a slim chance of closing out the season in top spot and remains a longshot despite registering his first career win in four meetings with Agassi in a two hour, 30 minute thriller.
If the year-end top ranking is to go to Switzerland for the first time not only must Federer capture the Masters Cup but current number one Andy Roddick must go winless through the round-robin stage while the other contender Juan Carlos Ferrero can win just once.
Seeing his first action since a semi-final
Federer got the contest off to the best possible start breaking Agassi at the first opportunity to pull ahead 2-0.
But the 33 year-old American quickly let Federer know his time away from the court had not dulled his competitive edge immediately breaking back then going on to take the set in a tie-break 7-3.
The 21 year-old Swiss, however, also had plenty of fight left after a long season taking the second set before clinching the match on his first match point in the third set tie-break 9-7.