The Portuguese looked technically superior on the ball but were made to work hard to defeat the young Joeys - who had taken the lead three times.
"We started well and controlled the pace of the game, we played some very good football and this allowed us to build up and score some good quality games," said Versleijen.
"Portugal increased the tempo in the second half and some mistakes and turnovers by us caused the goals.
"The players need to take the lessons learned and use them to learn for the following matches. The idea behind this tour is to play top quality matches before the AFC qualifiers in October and today was a high quality match that we had the opportunity to win."
The match was the opening game of a four-team tournament being co-hosted by Grimsby Town and Lincoln City.
England opened their campaign with a 2-2 draw with Turkey at Sincil Bank on Wednesday night. Australia will take on England at Blundell Park on Friday, with Turkey meeting Portugal in Lincoln.
The final games will take place on Sunday afternoon - with Glanford Park hosting England against Portugal, and Turkey meeting Australia in Grimsby.