The 34-year-old finished safely in the main pack on stage six which was won in a sprint finish by Belgium’s Tim Merlier.
Thomas remained third overall – 39 seconds behind race leader Simon Yates and 26 secs adrift of second placed Rafa Majka.
Sunday’s stage will be a lumpy one – an 181km stage from Pieve Torina to a tough, hilly circuit around Loreto with an uphill kick to the finish.
There will then be a final 10.1 km time trial in an out and back route around San Benedetto del Tronto where Thomas will be favourite for victory.
But it will depend on if he can overturn any disadvantage he will take into the final stage from Sunday’s mountain test.
I’m pretty happy with where I am, and it shows the work that I’ve been doing and that it’s been worth it. It’s encouraging and I think that this race will do me the world of good.”
Thomas is using the race between the seas as a test for next month’s Giro d’Italia and he looks to have returned to form ahead of his bid for a second Grand Tour crown.
Yates took the race lead on Friday’s stage five which he won by 35 seconds from Thomas.
“Today was quite easy I think, there wasn’t much fight for the breakaway and the sprint teams took it up straight away so was an easy day,” said Yates, the 2018 Vuelta a Espana champ, after stage six.
“I think tomorrow [stage seven] will be very hard, very difficult to control so we will try and defend as best we can.
“I can’t say I’ve ever looked forward to a time trial before but I’ll give it a good crack.”