Pantani was seventh fastest behind the Ukrainian in 54 minutes 33 seconds, but that performance was good enough to keep the quickest of his challengers at bay and leave him 44sec ahead of the field overall.
The defending champion's chief threat remained his fellow Italian, Paolo Savoldelli, who slashed his overnight deficit by 1min 21sec by clocking 53:12, only 17sec slower than Gontchar. Laurent Jalabert, the Frenchman who won the first time trial at Ancona, was third in 53:36, to cut his arrears on Pantani to 1:09.
"It was tough for everyone, because it was very hot," Pantani said after riding in temperatures up to 32C. "I couldn't have done much better than I did. It was important to not lose seconds, but just as important not to destroy myself because there are still four stages to go."
Neither Savoldelli nor Jalabert, formerly ranked No 1 in the world, can match Pantani's skill in the mountains, where the next three stages will be fought out. The tour ends on Sunday in Milan.
Ivan Gotti, the 1997 Giro winner and a strong climber, trails Pantani by 3:12, while Gontchar, who rides for the Vini Caldirola team, jumped from seventh to fifth overall on the strength of his success yesterday and now trails Pantani by 4:19.
Thursday's 19th stage of 166km (103 miles) takes the riders to Alpe Di Pampeago in the eastern Alps. It is one of the 22-stage race's toughest legs, featuring climbs to as high as 2,047m (6,755ft) above sea level.
As storms hit the Tour of Germany, Italy's Michele Bartoli and Emmanuel Magnien of France crashed badly.
Bartoli, the World Cup holder, fell heavily 75km into the first of the day's two stages, a 153.5km ride from Koblenz to Bensheim, and has undergone surgery for a broken kneecap and torn ligaments in his right leg. Bartoli will miss this year's Tour de France, though he should be fit for the World Championships in October.
A violent storm broke during the second stage, a 29.9km individual time trial, and Magnien suffered a spectacular crash. The Frenchman was riding through driving rain and gusty winds when he fell, and a press motorcyclist who was following the race crashed into him. Magnien was taken to hospital with a broken rib and a knee injury. Like Bartoli, he could also miss the remainder of the season.
Organisers said the time trial, which was completed by all the other riders and won by the Latvian, Raivis Belohvoscik, would not count for the overall standings. The German Jens Heppner, who is heading for overall victory in the tour, said: "It was crazy. I had never seen anything like it."
Another German, Erik Zabel, who has been beaten into second place on three stages by France's Jimmy Casper since the race began on Friday, won a mass sprint to take the morning stage, with Heppner finishing in the pack to retain his overall lead.Reuse content