Jalabert, who was passed by Pantani on the final climb the previous day, pulled away with less than 100m left. Pantani made a late charge over the closing 30m, but Jalabert edged across the finish first to claim his second stage win.
Italy's Gilberto Simoni was third. He also finished behind Pantani and Jalabert on Sunday, when Pantani solved mechanical problems to win the 15th stage.
In the overall standings, Pantani, an Italian who also won the Tour de France last summer, is 2min 5sec ahead of Paolo Savoldelli, with Jalabert another second back. Jalabert completed the mostly flat route of 232km (144 miles) east from Biella to Lumezzane across northern Italy in the unofficial time of 5:51.36.