Among Pogacar’s other expected rivals for the general classification, Colombia’s Daniel Martinez and Australia’s Ben O’Connor finished alongside Thomas in the peloton, while Spain’s Juan Pedro Lopez was a further 10 seconds back – 30 seconds behind in total.
France’s Romain Bardet, meanwhile, was 39th, one minute 37 seconds behind the leader.
While Pogacar is already in a strong position, stage winner Narvaez was delighted to deny him an eighth win in just 11 days of competitive racing this year.
“You don’t get many chances like that,” he said of taking the leader’s pink jersey.
“He [Pogacar] launched his sprint too early, after a hard stage like that he went from like 200m. I waited for the 100m mark.”
Sunday’s second stage is a 161km route from San Francesco al Campo to Santuario di Oropa (Biella) and includes a steep climb to the finish.