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.
Roglic leads Pogacar by 57 seconds with Friday's stage 19 and the culminating run up the Champs-Elysees on Sunday both set to be decided in a mass bunch sprint.
Egan Bernal has withdrawn from the Tour de France, his Ineos team said on Wednesday, after the young Colombian fell out of contention and complained of back trouble.
Lennard Kamna won the roller-coaster Stage 16 featuring five categorised climbs after pulling clear of a group of breakaway riders as the race entered the Alps on Tuesday.
Last year's winner Bernal dropped off the lead group on the long Grand Colombier climb and appeared to lose his chance of retaining the title as he dropped to 13th overall, 8 minutes 25 seconds off the yellow jersey.
Tour de France: Soren Kragh Andersen claims victory in Stage 14 as Primoz Roglic clings on to yellow jersey
After two sharp climbs and several attacks in the last 10 kilometers, Andersen broke away with three kilometres left to finish 15 seconds ahead of the chasing pack.
Tour de France 2020: Daniel Martinez cruises to victory in stage 13; Primoz Roglic extends overall lead
Defending champion Egan Bernal dropped time over the final kilometre of the 13th stage while Colombia's Nairo Quintana and Frenchman Romain Bardet also fell further behind Roglic.
Tour de France 2020: Marc Hirschi wins stage 12 after couple of near misses; Primoz Roglic remains on top of standings
Hirschi finally found the right formula with a heroic long-range solo victory on the Tour's longest stage of 218km
Tour de France 2020: Sam Bennett wins Stage 10 as Primoz Roglic avoids crashes to retain yellow jersey
After the 168.5-kilometre ride from Ile d’Oleron to Ile de Re, Roglic maintained a 21-second lead over defending champion Egan Bernal.
Tour de France race director Christian Prudhomme tests positive for COVID-19; all remaining riders negative
Prudhomme's positive test might have an impact on French political affairs as it came only days after he spent two hours in his car following a stage in the Pyrenees in the company of Prime Minister Jean Castex.
Yellow jersey holder Adam Yates and other Tour contenders, including defending champion Egan Bernal and favorite Primoz Roglic, crossed the finish line 6 minutes, 40 seconds later.
Ineos leader Bernal was in seventh place, trailing the currently irresistable Primoz Roglic by 31 seconds, with this year's Tour de France due to start on 29 August.
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.
Tour de France champion Egan Bernal's Team Ineos withdraws from all races over next three weeks amid coronavirus outbreak
Ineos riders had been scheduled to compete at six races before 23 March, including the prestigious Strade Bianche, the week-long Paris-Nice and the famed one-day classic Milan-San Remo. Bernal was set to defend his Paris-Nice title from 8 March
Laureus Awards 2020: Lionel Messi, Lewis Hamilton named Sportsman of Year; Simone Biles is Sportswoman of Year
Mercedes driver Hamilton won his sixth world championship in 2019, with 11 race wins and 17 podium finishes, while Messi was crowned the world’s best player for a record sixth time when he won the Ballon d’Or.
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
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: Egan Bernal sees lead trimmed by three seconds after mix-up in timekeeping during abandoned Stage 19
After climbing beyond his rivals in solo attacks on two consecutive Alpine stages, Bernal needs only survive a third one to seal victory in the 2019 Tour de France
Tour de France 2019: Egan Bernal takes yellow jersey from Julian Alaphilippe as hailstorm prematurely curtails Stage 19
Tour director Christian Prudhomme immediately announced that times would be taken at the top of the mountain, where Bernal was 2 minutes, 7 seconds faster than Alaphilippe, enough to wipe away the Frenchman's race lead