Sall was in Paris on Thursday and Friday for a global climate finance summit called by President Emmanuel Macron.
Sonko alleges that deadly clashes following his sentencing to jail time this month are the latest step in "a generalized and systematic attack on the civilian population" of Senegal since March 2021, lawyer Juan Branco told AFP late on Wednesday.
"It's ridiculous," Sall told AFP when asked about the legal complaint in France on Thursday.
This month's clashes over Sonko's conviction, for "corrupting" a young beauty salon worker, are the worst Senegal has seen in years, following a previous outburst two years ago when at least 12 died.
While the government toll for June is 16 dead, Amnesty International has counted 23 fatalities and the opposition tally stands at 30.
Opponents of Sall, first elected in 2012 and again in 2019, have been fired up by his evasiveness over whether he could run for a third term they see as unconstitutional -- following in the footsteps of other West African leaders in recent years.
Meanwhile Sonko's conviction will make him ineligible for the 2024 presidential election.
On a visit to Portugal on Tuesday, Sall also promised a "strengthening of democracy and freedom in Senegal, with respect... for the state of law" .
As well as the president, opposition leader Sonko's case targets Senegalese Interior Minister Antoine Diome, military police chief Moussa Fall and 112 others.
His criminal complaint has been filed with the Paris tribunal's crimes against humanity unit.
Sall and Diome have "ordered and supervised the commission" of crimes "against unarmed demonstrators since March 2021", including "murders, torture and forced disappearances", it alleges.
Lawyer Branco said he had identified "the murders of 50 people" since March 2021. He was to hold a press conference on the legal actions later on Thursday.
Under French law, filing a criminal complaint almost automatically triggers an investigation by a magistrate into whether the allegations are credible, although the process can be drawn-out and rarely results in criminal charges.
Sonko's separate request at the ICC in The Hague uses a provision that allows any person or group to ask for an investigation to be opened.