Seventeen of the 23 players picked by the German manager were in action at Wembley Stadium, with Mikel Obi, Kenneth Omeruo, Ogenyi Onazi and Ahmed Musa, who represented Nigeria at the 2014 World Cup in Brazil, heading to Russian Federation to appear at the finals for the second time. Kieran Tripper forced Francis Uzoho into the save, tipping it behind for a corner.
England "have a good chance of going all the way" at the 2018 World Cup, according to John Obi Mikel.
Gary Cahill powered home the opener on seven minutes before Harry Kane fired home with 39 minutes on the clock.
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.
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.
It was a night when England were more impressive in the first half and the second 45 minutes became uncomfortable after Arsenal'sAlex Iwobi pulled back a goal for the Super Eagles.
England will now seek to make it 10 unbeaten when they face Costa Rica, while Nigeria take on Czech Republic on Wednesday ahead of their big-kick off against Croatia in a fortnight. "By the time I was leaving, they had run out of stock again".
Crotone's Simy Nwankwo, who was a surprise inclusion to the 30-man list was announced as part of the players to the World Cup after convincing Rohr of his abilities.
- Alex Iwobi's goal was the first Nigeria have ever scored in an global match against England, in what is the third meeting between the two nations. England won the game 2-1.
But the England manager will also have to consider having another talk with Sterling after the City winger's latest controversy. His miss timed tackle gave Harry Kane the leverage to fire home the second goal of the match.