Winner of the 2018 Tour de France, Thomas' overall race ambitions were left in tatters after a fall on Monday saw him lose more than 11 minutes at the arrival at Mount Etna in Sicily.
Ganna, an Italian who rides for Ineos Grenadiers, beat Joao Almeida by 22 seconds on the 15.1-kilometer (9.4-mile) downhill time trial in Palermo.
The COVID-19 pandemic has played havoc with sporting events and current French government law limits gatherings to 5,000.
Tour de France: Former champions Chris Froome, Geraint Thomas left out of Team Ineos squad for upcoming edition
Froome has been trying to get back to peak condition after he was involved in a high-speed crash at last year's Criterium du Dauphine which came close to ending his career.
Geraint Thomas hoping Tour de France can go ahead in 2020, says he is in right shape to challenge for second title
The Tour, set to take place between 27 June and 19 July, has yet to be postponed or cancelled but with sporting events all over the world impacted by the coronavirus pandemic its chances of surviving as scheduled appear remote.
Coronavirus pandemic: LaLiga superstars try to stay fit amid lockdown imposed in Spain due to COVID-19
The coronavirus pandemic prompted the suspension of sporting events around the world, and forced athletes to find ways to stay fit. Quarantined countries like Spain were the most affected ones, and LaLiga teams have taken steps to keep players active while stranded at home.
Formula 1: Lewis Hamilton's absence from New Year’s honours list raises fresh debate over Briton's appreciation on home soil
Hamilton this year became the second most successful F1 driver of all time, and is poised to overtake Germany’s seven-times champion and Ferrari great Michael Schumacher in the record books
Road Cycling World Championships 2019: Great Britain's Geraint Thomas pulls out of men's team trial, to focus on team road race
Thomas remains in the six-man Great Britain team for Sunday's 285km road race from Leeds to Harrogate
Dutch newspaper Telegraaf said Dumoulin, ambitious to trade up his second place for overall victory in the 2020 Tour de France, would ride for the Jumbo-Visma team for the next three seasons
Chris Froome sets sights on record-equalling fifth Tour de France crown next year after crashing out of 2019 edition
British cycling great Chris Froome is determined to bid for a record-equalling fifth Tour de France crown next year after the horrific injuries he suffered in a crash ruled him out of this year's edition.
Tour de France 2019: Egan Bernal becomes first Colombian to win cycling's greatest prize, 2018 champion Geraint Thomas finishes second
Egan Bernal clinched victory in the Tour de France on Sunday, parading into Paris safely in the overall leader's yellow jersey, becoming the first Colombian winner of cycling's greatest prize and its youngest in more than a century.
Tour de France 2019: Geraint Thomas has 'defied all odds' to finish 2nd, says Team Ineos boss Dave Brailsford
Geraint Thomas has "defied the odds" by occupying second place in the Tour de France behind Colombia teammate Egan Bernal, said Team Ineos boss Dave Brailsford.
Tour de France 2019: Egan Bernal set to become youngest champion after defending overnight lead in penultimate stage
Egan Bernal all but clinched victory in the Tour de France, defending his overnight lead in the penultimate stage which left him only needing to cross the finish line on Sunday's twilight parade into Paris to become the first Colombian winner of cycling's greatest prize and its youngest.
Tour de France 2019: Italian Matteo Trentin wins Stage 17 via solo attack; Julian Alaphilippe retains yellow jersey
The breakaway split when Dutch rider Bauke Mollema accelerated at the front, a move that reduced the leading group to 10 members before Trentin made his move
Tour de France 2019: Caleb Ewan notches up second win of tour as Julian Alaphilippe maintains overall lead after stage 16
Caleb Ewan sprinted to his second victory on the Tour de France on Tuesday as Frenchman Julian Alaphilippe kept the overall lead after stage 16, where Geraint Thomas fell but finished with all the main contenders.
Tour de France 2019: Julian Alaphilippe says yellow jersey 'hanging by a thread' as race heads into final week
The 27-year-old Deceuninck-Quick Step rider, looking to become the first Frenchman to win the Tour since Bernard Hinault in 1985, told reporters on Monday's rest day that "the toughest is yet to come".
Tour de France 2019: Simon Yates wins second stage in four days as Julian Alaphilippe keeps overall lead
Thomas struggled on the final climb into the clouds, but then closed the gap on the leader to 1min 35sec by dropping him with a late burst afer initially looking like he was going to lose precious time on the overall leader.
Tour de France 2019: France's Thibaut Pinot wins stage 14 as Julian Alaphilippe extends lead over Geraint Thomas
French president Emmanuel Macron followed the whole stage from the lead car in the vast caravan and appeared animated as he was flanked on the podium by his two compatriots.
Tour de France 2019: Julian Alaphilippe wins stage 13 individual time-trial to extend lead atop standings, retain yellow jersey
As Alaphilippe made the 18 percent slope ahead of the home straight the noise was deafening as the victory over time-trial specialist Thomas unexpectedly materialised
Tour de France 2019: Britain's Simon Yates wins stage 12 as Geraint Thomas, Julian Alaphilippe finish together
Simon Yates is over an hour adrift in the overall standings, but punched the air in joy after outwitting his rivals to add this Tour de France stage to victories in the Vuelta and Giro