The 6ft 6in (1m98) winner Hoole timed 23 minutes and 27 seconds to bag a fourth stage from 10 for Lidl Trek, whose leader Giulio Ciccone is eighth overall, while Mads Pedersen won three stages for them in the first week.
"I'm so happy and there are son many people I need to thank. I just can't believe it," Hoole said after his second major win.
But rain fell heavily on the Tuscan course as the main favourites started coming down the starter's ramp, making the individual speed effort even more of a minefield than usual.
The 21-year-old Mexican Team UAE rider Del Toro who took the overall lead on the white gravel test on stage nine, lost 48 seconds to his team leader Spain's Juan Ayuso, who is now second overall at 25 seconds.
Italian home hope Antonio Tiberi of the Bahrain team is third at one minute and one second, while Simon Yates of Visma looked delighted when his chrono lifted him to fourth overall at one minute and three seconds with Primoz Roglic in fifth at one minute and 18 seconds.
Red Bull rider Roglic lost one minute and 15 seconds on Sunday and fell on his recon ride of the time trial Tuesday, so his performance at Pisa drags the former Giro and Vuelta champion back into contention.