Federer, who has now won all nine of his matches with Soderling, looked to be heading for an easy victory over the Swede when he raced through the first set in 20 minutes.
Soderling put up a better fight in the second set, breaking Federer in the sixth game, but the Swiss broke back immediately and again for a 6–5 lead before wrapping up victory with a second-serve ace on his first match point.
The 13-times grand slam champion will play either American James Blake or Croat Ivo Karlovic for a place in the quarter-finals.
Earlier, world number eight Fernando Verdasco continued his fine form and secured a berth in the last 16 with a 6–3 6–2 victory over fellow Spaniard Juan Carlos Ferrero.
Verdasco, who broke into the top 10 for the first time in February, has reached at least the last eight in all seven tournaments he has played this season.
The seventh seed broke Ferrero, a former French Open champion and world number one, five times on the clay at the Magic Box stadium and sealed victory on his second match point with a forehand winner.
Croatian wild card Ivan Ljubicic upset French ninth seed Jo-Wilfried Tsonga when he beat the 2008 Australian Open finalist 6–4 7–5.
British fourth seed Andy Murray beat Italy's Simone Bolelli 7–6 6–4 and will next play Spanish 16th seed Tommy Robredo, who put out American Mardy Fish 3–6 7–6 6–2.
Russian 10th seed Nikolay Davydenko beat Viktor Troicki of Serbia 6–2 6–2 in their first round clash.
World number one Rafael Nadal begins his quest for a sixth title this year, and fourth on clay, against Austrian Juergen Melzer on Wednesday.
