Gareth Southgate's side, who have one more friendly to come against Costa Rica on Thursday, begin their Group G campaign against Tunisia on June 18 and looked primed and ready on the evidence of Saturday's energetic outing.
Gary Cahill headed the hosts into a seventh-minute lead from Kieran Trippier's corner, the Chelsea defender eluding all of those bedecked in Nigeria's eye-catching colours.
After a week of being subjected to media scrutiny for his choice of tattoo and subsequent late arrival at the team's training camp, Raheem Sterling – who was booked for diving in the second half – had a sight of glory soon after the opener, but he miscued when one-on-one.
Despite seeing Sterling spurn another couple of promising openings, England did double their lead before the interval when captain Harry Kane's low drive squirmed underneath Francis Uzoho.
Nigeria halved the deficit two minutes into the second half courtesy of Alex Iwobi's cool finish after Odion Ighalo had struck the upright.
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.
Southgate, who was an unused substitute when England last met Nigeria at the 2002 World Cup, handed Jordan Pickford a start in goal, but the Everton goalkeeper was largely a spectator in the first half.
The home side won an early free-kick and Trippier's strike forced a smart stop from Uzoho.
But it was from the resulting corner that England took the lead, Cahill leaping to powerfully head home Trippier's outswinging delivery.
Sterling had a chance to write some more positive headlines when he raced through from Dele Alli's pass, but his finish was wayward.
The Manchester City star – who netted 18 Premier League goals for the 2017-18 champions – teed up Ashley Young for another England chance in the 19th minute, but his close-range effort was blocked and smuggled to safety.
A rapid counter-attack saw Sterling sent scampering into the box by Young, only for the former Liverpool winger's decision-making to let him down as he failed to pick out a team-mate.
Another opening came and went as Sterling fired over the crossbar before Kane got the second, his skidding effort somehow sneaking past the goalkeeper.
The Super Eagles needed a second-half response and quickly delivered after a change of shape to match their opponents, Iwobi side-footing in after Ighalo's shot came back off the post.
Sterling went in the book for taking an unnecessary tumble in the box and Eric Dier rose to head wide as England sought to reassert themselves.
Ultimately Southgate's charges did manage to restore order, holding onto their advantage with relative ease as the likes of Marcus Rashford, Danny Welbeck and Ruben Loftus-Cheek were afforded some game time late on, while Fabian Delph got his first international outing since 2015.
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.
Key Opta Facts:
- England are unbeaten in 18 encounters against African nations (W12 D6), with this the third time they've faced Nigeria – winning twice and drawing once.
- The Three Lions have conceded in successive internationals at Wembley for the first time since November 2013 (v Chile and Germany).
- Alex Iwobi's goal was the first Nigeria have ever scored in an international match against England, in what is the third meeting between the two nations.
- Gareth Southgate's men have only lost one of their last 21 games at Wembley Stadium (W16 D4), conceding just eight times in this run.
- England scored as many goals in the opening 39 minutes against Nigeria as they had in their previous four international friendlies.
- Harry Kane has scored eight goals in his last seven appearances for England, scoring at least once in six of those matches.