Bate and pilot Adam Duggleby went quicker than ever before in the 4,000m tandem pursuit but still saw their colours lowered by Flying Dutchmen Tristan Bangma and Patrick Bos.
The silver-medallist Scot will now look to next weeks’ time trial road event, in which he is both the Paralympic and world champion.
And it's fair to say the tandem duo are smarting, Duggleby admitting an issue with pacing in their qualifying race cost them dear in the final.
"That's what you call a classic kicking, we did what we could but it wasn't enough, their performance was phenomenal and sometimes you need to settle for second," said Bate.
"Emotionally it's disappointing but logically we need to be realistic. We gave everything we had, it just wasn't good enough. "I'm just pleased to be standing here with a medal because it could have gone a lot worse. It's never nice losing but when you get a canning from a bike like that you can still be proud. It's a medal, just not quite the right colour.
"We can reset for the time trial now, it's a brutal course, especially in this heat, but we know it will suit us."
Neil Fachie and pilot Matthew Rotherham always knew this event was about preparation for Saturday's blink-and-you'll-miss it 1000m time trial.
They are the defending world champions in that event while Fachie, the gold medallist from London 2012, still fumes about his silver in Rio.
"I'd be surprised if our event isn't won in a world record time, that's what we are anticipating and what we're aiming for," said Aberdeen's Fachie, 37, who made his Paralympic debut in Beijing in athletics before switching to cycling.
"A lot of good preparation has gone into the Games and this was really just a chance to run through it in a race environment. We had a couple of technical issues that we'll have to correct for Saturday but we're in a great place and I can't wait to get going on our main event.
"We came in here with the kilo in mind and we probably didn't attack it as hard as we could, as a racer you want to give your all but we didn't want to destroy ourselves here and cost ourselves on Saturday.
"The holding camp was a dream and everything went to plan, since we've been here we've found some extra speed and got quicker and quicker.
"I've never been in better shape, we've done everything right and it's just a waiting game - it's frustrating because we want to show the world what we are capable of. We feed off the big game and that's coming on Saturday."
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