How about using oxygen?
The Jedi will likely notice you reducing the oxygen, but if you increase pressure in the room and change the air to a higher oxygen purity you'll induce hyperoxia or oxygen toxicity: https://en.m.wikipedia.org/wiki/Oxygen_toxicity
This causes disorientation, spasms, near-sightedness and more, more than 15 minutes of exposure is more than enough to incapacitate them. As far as I can tell age and bodyweight have little effect on the effects so this is indoscriminate as long as all subjects are equally active.
Otherwise there is almost nothing that will work. Here's the wiki about gasses that cause sleep, unconsciousness or other forms of incapacitation: https://en.m.wikipedia.org/wiki/Incapacitating_agent
It specifically states that the US for example looked at ways to knock out hijackers of aircraft but found none that guaranteed survival of the hostages as agression or hazards of the gas itself can kill, such as during the 2002 russian hostage situation where 15% of 800 hostages died after exposure to the (unknown) gas. Considering the amount of targets (2 Jedi), their similar physiology (both grown and trained adults) and that you can immediately offer proper medical assistance the chance of death can definitely be reduced.
I would discard the notions of some of your other advisors, mainly the one of "the dosage to knock out vs kill differs from person to person therefore you cannot use it". While true, the margin of error depends on your targets and gas used. If you have a 7 foot tall Jedi bodybuilder in the prime of his life with a 6 year old padawan the chance of over or underdosing either one is huge, if they are of similar build and age you calculate the potential dosage to knock out the one with the least bodyweight, reduce that dosage a little and use a gas that incapacitates or reduces capabilities before that to make sure neither one will die but they are easier to capture.
Edit: The only other solution is oxygen deprivation by sucking the air out, rather than deprivation by replacing oxygen. If you simply replace the oxygen and your oversensitive Jedi notice it, they put on those rebreather thingies and escape. But if you suck the air out to a low enough content then their best bet is to exhale as much air or their lungs might burst, and they'll lose consciousness quickly. (https://www.scienceabc.com/pure-sciences/what-happens-to-a-human-body-if-exposed-to-the-vacuum-of-space.html).
The beauty of this is ofcourse that you can announce it to your Jedi: "hey we'll suck the oxygen out now thank you". The Jedi will try to survive as long as possible and exhale. Now you'll lower the oxygen content slow enough that lung bursting won't be a problem as the Jedi will lose consciousness before that, but they won't know that! The best part is that if you get the room pressurised and oxynegated quickly they'll not have any permanent damage, as evidenced by both some rather nasty experiments with dogs and an unlucky astronaught who had an accident inside a chamber, lost consciousness and made a full recovery. Within that time period that your Jedi are still unconscious or recovering from it, you can easily sedate them with something in the bloodstream and then just hook them up to some aneastetics to keep them under until you have them bound, not gagged so they can make quips about their terrible situation and you fail to search their body's so they have something hidden to cut the ropes and make a daring escape as you leave them in a truly deadly situation but don't watch them die (ropes on your space station? Why ofcourse! I put them next to my goatee oil!). I was going to interrogate them? Oh I'll forget about all that as I'm practicing my moustache twirling and make some exposition about my masterplan of ruling the planet by forcing the queen to sign a peace treaty after having her walk through a city with minimal protection and using convoluted politics.
