The Nigerian marking was poor and the West Ham defender had little difficulty nodding in his second goal for his country.
Goalkeeper Austin Ejide caused a few flutters on the Nigerian bench when he made a hash of a McCann cross and it needed Isaac Okoronkwo to hack the ball clear.
Ejide made amends soon after, blocking a Paul Lambert shot from a tight angle.
The World Cup qualifiers had been sleepwalking through the first half hour and it took a moment of magic from Kanu to wake them from their slumber.
The Arsenal man wove his way past a number of Scottish defenders and it took a wonderful save from Rab Douglas to stop his low angled shot.
Bartholomew Ogbeche then fired wide after turning David Weir and Kanu came close with a header from a Jay-Jay Okocha free-kick.
Ogbeche forced Douglas into another good save after Stockdale had lost possession.
In the 40th minute Aghahowa leveled the scores from close range after a Crainey tackle on Kanu had rolled into his path.
Immediately after the re-start McCann burst through the Nigerian defence on the left but his shot from a wide position was saved - with Thompson screaming for the ball in the six yard box.
Both sides took the opportunity to field a number of substitutes and the free-flowing football of the first half was disrupted.
The home side looked tired after their early exertions and the classy visitors made them pay in the 69th minute with a quick counter attack which lead to Aghahowa's second goal of the evening.
Crainey was bypassed by a long ball from Okoronkwo and Ikedia had time and space to measure his cross for the Shakhtar Donetsk striker to arrive from deep and head powerfully past Douglas.
Substitute Michael Stewart saw his low shot gathered by Ejide and the keeper had previously been quick off his line to deny McCann and Garry O'Connor scoring chances.
Scotland: Douglas, Stockdale, Weir, Dailly, Crainey,
McNaughton, Williams, Lambert, Gemmill, McCann, Thompson. Subs:
Gary Caldwell, Davidson, Johnston, Alexander, Stewart, Crawford,
O'Connor, Ross, Combe, Paul Gallacher.
Nigeria: Ejide, Sodje, Yobo, Okoronkwo, Christopher, Okocha,
Ejiofor, Utaka, Nwankwo Kanu, Aghahowa, Ogbeche. Subs: Bankole,
Eze, Ifejiagwa, Kaku, Mancha, Akwuegbu, Ugali, Adepoju, Lkedia,
Referee: Tom Henning Ovrebo (Norway)