It was the third straight time he lost to Nadal in a Grand Slam final and Federer was beginning to believe this Spaniard might keep him from surpassing Pete Sampras for the most major titles in men's tennis history.
But then Nadal struggled with injuries and Federer was able to win his record-tying 14th, record-breaking 15th and one more for good measure.
When Nadal returned to full strength in 2010, Federer was starting to hit the twilight of his career, failing to reach the semifinal of a Grand Slam for the first time in six years, and the two have not met at a major since.
They've played five times outside of the Grand Slams, with Federer winning two meetings, including a straight-sets victory on the clay of Madrid right after that 2009 Aussie Open loss.
Federer even took a set from Nadal at the same event last month before dropping the next two.
Many believe the 29-year-old is already the best player of all time, but there would be no hold outs remaining if he were able to beat maybe the best clay court player ever in his prime at the French final.
Few thought Federer would even get past the red-hot Novak Djokovic in the semis. The Serb had won 43 straight matches, including three in a row over Federer, but the pressure of reaching No. 1 in the world for the first time had he won was too much for Djokovic and the veteran's championship experience won out.
Now the Serb will root for Federer, because if Nadal loses, Djokovic becomes No. 1 anyway.
But Federer has so much more on the line.
Follow me on Twitter at @ JordanHarrison.
Jordan is one of Bleacher Report's New York Yankees and College Basketball Featured Columnists.
He can be reached at email@example.com