Bruno Alves' first-half red card for a dangerously high challenge on Harry Kane altered the nature of the fixture at Wembley, but England struggled to break down the visitors until Chris Smalling's 86th-minute header settled the match.
But Hodgson insists he is happy with the preparation his side have undergone ahead of their opening Euro 2016 against Russia on June 11.
"The two-and-a-half weeks we have been together have been good, and I am happy that we are definitely on the right track.
"We will go to France confident and, while we're not the finished article, there are a lot of teams that are not the finished article. If we'd won all the games 4-0, there might have been talk we'd walk through the tournament, and with a young squad it would have been too much pressure."
Hodgson did admit that he would have preferred the Portuguese to have stayed at full strength, while also adding that he was happy enough with the shape of his attack despite Jamie Vardy and Harry Kane spending much of the game in wide attacking positions.
"I was disappointed it didn't stay 11 against 11 because we wanted to know how we might deal with them rather than go up against a packed defence. But there were a lot of positives in terms of good individual performances, and going into a tournament with three wins on the spin is a bonus," he added.
"When you play with that system you need your strikers to spin, they were defending the wide areas. [Too wide?] Not really, no. There may have been a few moments they were too wide but largely it was good. They were encouraged to split wide but also come in."