Thomas placed fifth overall at 58 seconds behind the Colombian one year after he won the Paris-Nice stage race. He lost 1-22 minutes on day one when Gianni Moscon's front wheel collapsed. Reportedly, Diego Rosa's and Mikel Landa's wheels also failed.
"Sky and Thomas were very unlucky in the team time trial and they would have been a serious rival without that incident on the first day, they'd have been a lot closer," Quintana said.
"In the Giro d'Italia, we'll have to keep a very close eye on him and not just him, also the rest of his team-mates, who will be preparing for this big race very seriously."
Quintana won the overall with 25 seconds over Rohan Dennis (BMC Racing) and 36 seconds over Thibaut Pinot (FDJ).
Thomas attacked the following day on stage two and won the uphill finish to Pomarance. On Saturday, he attacked with Quintana in the summit finish up Monte Terminillo and placed second.
On Monte Terminillo, just like two years ago in a snowstorm, Quintana clinched the overall lead with his stage win.
"It's been more difficult to win Tirreno-Adriatico two years ago when I had more rivals who were more experienced than I was," he said.
"Now I'm stronger and smarter. I also had a better team this time around. I won more with my head than with my legs."
Quintana warned press before talking that he had to be quick because he had a flight to catch. He will return home to Colombia, where he will rest and build up to the Giro d'Italia at altitude.
He will travel back to Europe in late April to race the Vuelta Asturias before the Giro, May 5 to 28. In the Giro, he will face Thomas again.
"I've finished this race in better shape than when I started. I'm still building upwards, and I'm very pleased because I'm in good shape and have done good work for the future races," Quintana said.
"It's difficult to name my rivals. Nibali, for example, is always at a high level, it's a home race for him, and so is Fabio Aru. They're always strong there, that's an objective for them they always fulfil.
"Other rivals? Geraint will be very strong, and there are sure to be others. But the Giro is very different, and some riders who weren't so good here, will be building."
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