You can now use your iOS device to pay for your fare on Toronto's Up Express, which connects Downtown Toronto with Toronto Pearson International Airport. It will work to pay for adult fares, but you'll still need a Presto card for student or senior discounts.
According to Metrolinx, you have to make sure to avoid "card clash" when paying via Apple Pay. If you tap on using Apple Pay on your iPhone, you'll need to tap on again when you get off at your destination using your iPhone. Don't use other Apple Pay-supported devices on the same trip (like your Apple Watch). Onboard, you will also use your iPhone to get your ticket verified.
You can preset your preferred credit card on your iPhone for easy access. It will support Visa, Mastercard, or American Express credit cards as part of this pilot.
Source: 9to5Mac