From the corner in the 10th minute, England got their first goal.
England have been pitted in Group G with dark horses Belgium, Tunisia, and debutants Panama but fans are sceptical about the country's chances following a disastrous 2014 campaign.
Super Eagles' Technical Adviser Gernot Rohr has declared that the technical team of the three-time African champions took many positives away from Saturday's friendly against England at Wembley despite coming short by two goals to one against the Three Lions.
Rohr made four changes at the break and the substitutions were having an immediate impact as the Super Eagles had England on the ropes inside the hour-mark.
Captain Kane, who scored his eighth goal in his last seven appearances for England, told ITV: "It was a good win against a tough side".
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Nigeria was looking for a second goal right until the final whistle with England working hard to see out the match, but ultimately it was the hosts who claimed a hard-fought win in preparation for the upcoming World Cup in Russian Federation.
"That five, six-minute spell is what we must learn from because that could be enough to put you out", he warned. We were excellent in the first half and created a lot of chances.
Southgate still has time to work on those tactical issues as England have one more friendly - against Costa Rica in Leeds on Thursday - before they fly to Russian Federation for their Group G opener against Tunisia in Volgograd on June 18.
Following an inconsistent season with Tottenham and some diffident displays for England, Alli needed to cement his place in Southgate's team and, ignoring the hail of boos, he was making a convincing case. But the visitors made their changes in the second-half and made a game of it.
"Saturday was a really disappointing game for us, especially for me in the first half".
But the game was little of a true test for England, who benefited from a string of first-half errors by Nigeria.