Verstappen, who was third behind Hamilton and the Briton’s Mercedes teammate Valtteri Bottas in the 2020 championship, timed a best lap of 1:28.960 on Sunday.
That proved to be the fastest time of the three-day session.
However, rookie Yuki Tsunoda, the first Japanese driver to compete in Formula One since Kamui Kobayashi in 2014, also laid down a marker.
His time on Sunday of 1:29.053 in his AlphaTauri was the second best overall of the week.
Verstappen had also topped the charts on Friday on the opening day at the dusty Sakhir circuit which will also stage the season opener on March 28.
“They are looking strong,” said seven-time champion Hamilton.
“They’re going to be a different machine or animal this year with, I think, a really good, strong line-up for two…