The teams were charged two weeks ago and UEFA's Control, Ethics and Disciplinary Body (CEDB) met on Thursday to decide their punishments.
City has been slapped with a €15,750 (£13,000) fine for the throwing of objects in its 2-0 win over Dinamo Zagreb on 1 October.
Dinamo has also been ordered to pay €20,000 (£17,300) for the same offence and acts of damages in the away end at the Etihad Stadium.
Liverpool was sanctioned to the tune of €10,000 (£8,600) after its supporters came onto the pitch during and after their 4-3 Champions League win against Salzburg at Anfield on October 2.
A group of youngsters climbed over the hoardings at full-time and ran towards Andy Robertson to collect his shirt, while another spectator entered the pitch midway through the second half and was led away by stewards. Salzburg were fined €3,250 (£2,800) over the throwing of objects.
Ajax must pay a total of €68,000 (£58,800) in fines. Acts of damages and crowd disturbances from the travelling fans at Mestalla has resulted in a ban from selling tickets for their trip to Chelsea on November 11, while they must contact Valencia within 30 days and agree compensation.