BMC Racing's Dennis inherited the overall leader's white jersey from opening stage winner Dylan Groenewegen (LottoNL-Jumbo), who lost 51 seconds over the 9.6km course in Breda in the Netherlands.
"From what I saw from my side, it was as close to perfection in a time trial," Dennis said. I took all the risks and kind of crossed my fingers ever time I went through a corner. But it worked out. Today was as quick as I could go."
The 26-year-old Dennis now leads the overall standings by five seconds from Jos Van Emden (LottoNL-Jumbo) and 13 seconds over Peter Sagan (Tinkoff).
The result was a good marker for Dennis ahead of the 9-16 October UCI Road World Championships where he will be counted among the time trial favourites for a podium placing.
"Today's performance was good for confidence when it comes to Qatar," Dennis said. I was a little bit worried before coming here.
"I thought that maybe because I've lost weight since Rio, maybe I've lost that raw power that I had when I was a couple of kilograms heavier.
"It's flat, there are corners here in the time trial and it was all about who had the most power today so that's a good indication for Qatar, considering that's going to be 100 per cent flat."
The third stage is a 186km ride between Blankenberge and Ardooie in Belgium. The Dutch-Belgian race concludes on Sunday.