Tolls

The second toll station expected you to insert the ticket you received at the first one, to calculate the exact toll based on the travelled distance. As you did nothing, the machine tolled you according to the max possible distance on that road.

Why shouldn't you pay and ignore a legitimate toll? At least ask how you can get it reduced.

The yellow lanes called Tellepass are reserved to those who use a transponder to pay tolls. Lanes that I'm sure your guide told you not to use if there is another option.

The company that manages the italian motorway network is called Autostrade.it, the site has an English version and a page about fines & unpaid tolls.

If you didn't purchase a Telepass transponder you were in the wrong lane

First of all there are no toll bridges between Pisa and Perugia. My suspicion is that you entered the A1 freeway (a toll freeway) at FIRENZE SCANDICCI, coming from Pisa on the FIPILI freeway (no toll), then you exited the A1 at VALDICHIANA exit near Bettolle.

So, you should have picked up the ticket at FIRENZE SCANDICCI toll booth and used that ticket to pay toll (based on distance traveled) at VALDICHIANA. Instead you entered the freeway on a lane reserved to people with transponders and exited through a lane where you were suppose to hand the ticket and insert money or credit cards.
Sounds you did some Mr. Magoo driving in Italy.
If you ignore the toll, it will go to the rental car company. They will simply add it to your credit card on file. Certainly with plenty of extra fees added to it.
If you ignore it, please come back here a few months from now and tell us how it went. If you get away with it, I'll di the same next time I go.

Thanks for the replies.

Do I owe money to both Autoslade and Telepass then? And how can I pay?

Lesson learned.

https://www.autostrade.it/it/rmpp

You can pay above, but you need all car info (like license plate, entrance, day, time, etcthere is the English page.

Is there a deadline for payment?

Also, do I owe Telepass anything?

Forget the telepass. Use the ticket you got when you entered (at telepass lane?) to determine the entrance station and the ticket you received at the end as exit station.
Post it here if you want and we can see on line how much you owe.
Then you go on line and you enter that info:
Car plate, date, time, freeway, entry point, exit point, and pay with a cc.
If you pay within 15 days I don’t think they have extra fees.