The Swiss equalled Pete Sampras's record of 14 grand slams, becoming only the sixth man to win all four major tournaments after sealing victory in just under two hours.
"It was really not easy to deal with my emotions," said the 27-year-old Federer, who lost to world number one Rafael Nadal in the three previous finals.
"It might be the greatest victory of my career."
The 23rd-seeded Soderling had ended Nadal's four-year reign on the Paris clay in the fourth round.
"To me, he is the best player in history," the Swede said.
Federer, the second man after Andre Agassi to win all four grand slam titles on all surfaces, started the match confidently by racing into a 4-0 lead.
Soderling held serve for 4-1 but Federer, who had never lost to Soderling in nine previous matches, kept up the pressure and clinched the first set on the Swede's serve with a crosscourt passing shot.
The match was briefly interrupted after a man came on to Centre Court with a red and blue flag during the fourth game of the second set.
He jumped from the stand opposite the media box and approached Federer, touching him with the flag and trying to put a hat on his head.
Leaping over the net towards Soderling, the man was tackled by Roland Garros security officers and carried away from the court.
Federer lost three points in a row after the incident as Soderling levelled for 2-2.
"It was clear that he was not going to do anything to me, but what is 'normally' nowadays?," Federer told French TV channel France 2.
"It is difficult to stay calm in such conditions. Maybe I should have taken a two-minute break after that game."
Both players held serve to a tiebreak which Federer cruised through 7-1 after serving four aces.
The Swiss broke in the first game of the third set when his opponent sent a forehand wide and he never found a solution to turn the situation around.
Federer ended his wait on the first match point when Soderling netted a service return and the Swiss fell to his knee in tears, triggering a deafening roar from the 15,000 crowd.
Federer said he would never again feel any pressure in his career. "It takes away so much pressure. Now, I can play in peace for the rest of my career.
"Nobody will never tell me again that I have not won Roland Garros."
Federer was presented with the Musketeers' Cup by Andre Agassi, the only man before him to have won the four grand slams on all surfaces.
"That he gives me the trophy, it's too much, it was very nice of him to come here this year," Federer said. "He told me 'it seems like it's destiny for you, you deserve it'."
Federer thanked the crowd for their warm support throughout the tournament.
"It feels good to be on the podium as the winner for once," he said.
Swiss Master on top of the world
* Born Aug. 8, 1981 in Basel, Switzerland
* By winning 2009 French Open crown he becomes only the sixth man -- after Fred Perry, Don Budge, Rod Laver, Roy Emerson and Andre Agassi -- to have won all four grand slam titles during their careers.
* Fourteen Grand Slams: French Open 2009; Wimbledon, 2003-2007; US Open 2004-2008; Australian Open 2004, 2006, 2007
* Men's Grand Slam title leaders: 14-Pete Sampras (US) and Roger Federer (Switzerland). 12-Roy Emerson (Australia), 11-Bjorn Borg (Sweden), Rod Laver (Australia), 10-Bill Tilden (US).