Chris Smalling headed home Raheem Sterling's cross four minutes from time for a maiden international goal against a side reduced to 10 men for 55 minutes after Bruno Alves was punished for kicking Harry Kane in the head with a flying challenge.
England found it difficult to break Portugal down thereafter, however, struggling for fluency and creativity, and Rooney did not allow Smalling's late intervention to paper over the cracks.
"We won the game but it was always difficult. They went to 10 men and that [struggling against depleted opponents] can happen in football," he told ITV.
"We kept going and we got the win. That was obviously important to us. I thought we were the better team, I thought even at 11 v 11 we were the better team.
"We need to play better, we know that. But it's a good sign when you don't play as well as you can do and you win the game."
Rooney lined up in the same England starting XI as strikers Harry Kane and Jamie Vardy for the first time and the attacking trio largely failed to fire, with the Tottenham and Leicester City stars too often confined to duties out wide.
Hodgson's skipper confirmed that forward line-up is under consideration for next weekend's opening Euro 2016 Group B match with Russia but insisted England's destiny will be decided by more than three players.
"We didn't have many chances, any of us. It's something the manager is working on and Portugal made it difficult," Rooney explained.
"There are 23 men in the squad, it's not three players. It's 23 and it's about all of us."
"We've made a lot of changes to the team and we haven't been at our best but we have won the three games, which is important - especially for a young team."