But Gernot Rohr's men could not force their way through again and England improved their record at Wembley to just one defeat in the last 21 matches.
Alli (whose full first name is Bamidele) was eligible to represent the African nation through his Nigerian father, but chose to throw his lot in with England where he was born and has lived all his life. But after that we dealt with it well.
'The front four, some of the movement and interplay, we looked a threat with plenty of pace.More news: Kim Jong Un sends Trump 'very nice' letter - and it's huge
Ben STANSALL / AFP Nigeria's German manager Gernot Rohr (C) speaks to his players on the pitch after the worldwide friendly football match between England and Nigeria at Wembley stadium in London on June 2, 2018. It was a decent exercise for us to adjust to that.
"Dele [Alli] and Jesse [Lingard] made unselfish runs".
"Saturday was a really disappointing game for us, especially for me in the first half".
Alex Oxlade-Chamberlain was impressive this season for Liverpool, playing on the right-hand side of a midfield three but a knee injury has ruled him out of the tournament, making room for Lingard and Alli to play as the two slightly more advanced midfielders.More news: Merkel gives new push for eurozone reforms ahead of European Union summit
"In the second half they scored and it puts the pressure on but we got back into it and kept the ball and came back well".
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.
The Three Lions made a couple of changes of their own in the last quarter of an hour but their effect was that they slowed the tempo of the match.More news: IPhone battery health menu first look