Hart pulled off some decent stops and had little chance with either of the visitors' goals as the England number one made a steady return to club action having recently been dropped by Manuel Pellegrini in favour of Costel Pantilimon.
"Nothing's changed for him," City midfielder Milner told Sky Sports. "He keeps going, keeps working hard.
"He's pulling off great saves in games when he's getting opportunities. He's a great pro and he knows he's just waiting for his chance and hopefully he can take it when it comes."
Hart's return was one of a number of changes made by City with their place in the last 16 already having been secured.
Sergio Aguero and Samir Nasri scored City's opening two goals but they were cancelled out first by Tomas Horava and Stanislav Tecl.
But City made sure of the win thanks to goals from Alvaro Negredo and Edin Dzeko.
The number of changes made by Pellegrini appeared to affect the home side's performance, but Milner stressed the importance of City utilising their reserves of talent.
"We're a squad and we're going to need all of the squad to win anything," he said.
"It's important everyone contributes when they play."
The win maintains City's hopes of topping Group D and continued their free-scoring form at the Etihad Stadium, where they have now netted 22 times in their last four games in all competitions.
And Nasri knows that level of performance will be key if they are to go even further into the competition come the new year.
"After the knockout stage it's important to win at home," he told Sky Sports. "We'll try and continue in this way."
Discussing the performance against Plzen, he added: "It was a hard game. We know there is no easy game in the Champions League.
"It was important to finish at home with a win in the group stage."