While Portugal captain Cristiano Ronaldo was rested following his involvement in Real Madrid's Champions League final victory over Atletico Madrid last weekend, England manager Roy Hodgson was effectively able to name a full-strength line-up.
But with his side's Group B opener against Russia in Marseille just nine days away, it took Smalling's first international goal to secure victory after the hosts had toiled badly despite playing against 10 men following the 35th-minute dismissal of Bruno Alves.
"I'm not prepared to stand here and criticise some players. If I start being dissatisfied with three wins against Australia, Turkey and Portugal, I'm going to be a hard coach to satisfy."
Nonetheless, despite having managed to prevail in all three of their pre-tournament friendlies, England will travel to France on Monday accompanied by more doubts than certainties.
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There was little for Portugal's supporters to cheer on a chilly night in west London as their team lost to England for the first time in six games, but coach Fernando Santos will have Ronaldo back in his ranks for their final warm-up match against Estonia in Lisbon on June 8.
England's fans have been clamouring for Wayne Rooney,
Harry Kane and Jamie Vardy to be aligned together in attack, but although Hodgson selected the trio in the same team for the first time, Kane and Vardy took up wide positions, with Rooney in the centre.
With newly appointed Manchester United manager Jose Mourinho in attendance, keeping a close eye on new charges Rooney and Smalling, as well as his Portuguese compatriots, the initial chances England created stemmed from right-back Kyle Walker.
The momentum lurched in England's favour 10 minutes before half-time when Fenerbahce centre-back Alves was shown a straight red card for a dangerous, head-high challenge on Kane near England's right-hand touchline.
Fortunately, the Tottenham striker emerged unscathed and shortly after he worked Patricio with a drilled shot from Rooney's pass.
It was a measure of the tedium in the second half that it took nearly 20 minutes for either team to muster a shot on target, with Eric Dier curling a long-ranger straight at Patricio as a Mexican wave rolled lazily around the ground.
Portugal substitute Ricardo Quaresma gave England a scare by curling a shot just wide, but with four minutes remaining Raheem Sterling crossed from the left for Smalling to head in the winner.