Team Mitchelton-Scott's Brit gained another six seconds on Dumoulin (Sunweb) on Wednesday with the short, but sharp climb to Osimo in Marche. Dumoulin charged after Yates's attack in the final two kilometres, when the pitches reached 16 per cent, and was within two seconds at the finish line.
With the time bonus, Yates gained six seconds and moved to 47 seconds ahead of Dumoulin. Frenchman Thibaut Pinot (Groupama-FDJ) sits at 1-04 in third.
For Yates, it is worth spending extra energy to gain time on stronger time trial rivals. Dumoulin, the world champion, is looking for payback on Tuesday when the race covers 32.4 time trial kilometres to Rovereto.
"No, no," Yates said when asked if he is worried about using too much energy now. "They have to follow me so for sure they are on the limit. Well I hope so! I hope they are not holding anything back! Otherwise, I'd be very worried.
"I'll keep needing to do this. If I explode in the final week, so be it because I need to gain time and I'll keep trying."
Yates has a healthy 47 seconds over Dumoulin, but says he'll need more to be assured of a decent buffer in the race against the clock.
"At a minimum, I need two minutes," he continued. "But I'd prefer much much more."
Dumoulin gained 20 seconds on Yates on the short 9.7-kilometre time trial in Jerusalem on day one. Since then, on the mountain finishes he has been losing time.
On stage 11, however, Dumoulin was the best of the rest and charged after Yates when his rival attacked.
"I thought, 'Who's chasing me all the way in the final!?' But at least I have two seconds. I'm happy with that," Yates said.
"There are many rivals still and they are close to me, but Tom is the one I'm afraid of because with the TT yet to come it's going to be difficult to beat him."
"I don't know, I really don't know," Dumoulin said of how much time he could gain in stage 16's time trial to Rovereto.
"I never look at time differences, I just go full-gas until the finish of the time trial and I will see what I get. But first there's this weekend."
The Giro d'Italia climbs the 22 per cent pitches of Monte Zoncolan on Saturday and faces another heavy mountain day on Sunday to Sappada.
"The differences are not so big yet, 47 seconds is not a lot, but it's already quite much if I lose more time on the Zoncolan or the day afterwards, so then it would be very difficult," Dumoulin explained.
"But Fabio Aru, Froome and all of the other guys who are now in the top-10, they are definitely not out of contention yet. A lot can happen in the coming weekend and the last week."
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