Fonte was introduced as a substitute before half-time to bolster the Portugal backline after fellow defender Bruno Alves was sent off for a reckless head-high challenge on Harry Kane.
The Southampton man impressed alongside the veteran Ricardo Carvalho in repelling England's forwards, leaving opposition centre-half Chris Smalling to steal victory with a well-taken header four minutes from time.
Much of England's attacking play was unconvincing as new-look front three Wayne Rooney, Jamie Vardy and Kane struggled for fluency but Fonte believes the Three Lions have what it takes to impress in France.
"I regard England as one of good champions, obviously," he told ITV. "When you look at the front five that they have, you look at the young talent that they have.
"They have players with the experience of Rooney so you have to look to England and expect something good from them.
"They have a lot of quality but there are other teams as well. It will be interesting, it will be a good Euro, but England definitely have the quality to go far.
Portugal conclude their Euro 2016 preparations against Estonia next week, where coach Fernando Santos could recall Cristiano Ronaldo after resting his superstar captain for Thursday's largely forgettable encounter.
"It's disappointing. It was tough to play against 11 when we were one man down with the quality that England have," Fonte added
"But we take the positives. I thought we defended well - compact. They didn't create many, many chances in the second half.
"We actually had two good chances to nick a goal. We're disappointed but we will take the positives and come out of this stronger."