MacDonald, who has played in 29 Tests since making his debut against Scotland in 2000, beat his fellow utility back after impressing most in NPC action this week.
MacDonald's Canterbury retained the Ranfurly Shield against Bay of Plenty, although McAlister played a pivotal role as North Harbour won in Wellington.
National team coach Graham Henry brought in McAlister for the last Test that Carter missed - the third British & Irish Lions match in Auckland.
Henry based his decision on form, saying: "Leon played exceptionally well for Canterbury at the weekend.
"We also looked at the combination between nine and 10 and felt it was better to opt for experience in this Test."
Piri Weepu retains the half-back position, with Byron Kelleher continuing his recovery from concussion.
Kelleher initially joined the squad in Dunedin for a medical assessment, but then returned home. Kevin Senio will deputise again.
Auckland winger Doug Howlett, recalled for the Test, is expected to start on the bench.
New Zealand team: M Muliaina, R Gear, T Umaga (Captain), A Mauger, J Rokocoko, L MacDonald, P Weepu, T Woodcock, K Mealamu, C Hayman, C Jack, A Williams, J Collins, R McCaw, R So'oialo.
Replacements: D Witcombe, G Somerville, J Ryan, S Lauaki, K Senio, L McAlister, D Howlett.