The left-hander scored a 121-ball 80 with four sixes and eight boundaries to steer the Kiwis to 244-8 declared in reply to Pakistan 'A' first innings total of 215 all out.
At stumps Pakistan 'A' had made 13-1 in their second knock, with opener Shan Masood dismissed for four by paceman Neil Wagner, still trailing by 16 runs.
Sami Aslam was six not out and Abid Ali was still to get off the mark.
Anderson added 57 for the sixth wicket with BJ Watling (37) after top order did not bat for long to get tune up to the conditions ahead of the first of three Tests against Pakistan starting in Abu Dhabi from Sunday.
Anderson, 23, played last of his seven Tests in February this year and was not part of the team for the West Indies tour in June.
Openers Tom Latham (15) and Luke Ronchi (16) fell within 17 overs while Kane Williamson made 28 with four boundaries and a six.
Key batsman Ross Taylor, recovering from a right calf strain, made 11 while Tim Southee chipped in with 28.
For Pakistan 'A' seamer Anwar Ali (2-15) and off-spinner Junaid Illyas (2-44) shared the bowling honours.
Earlier leg-spinner Ish Sodhi added one more wicket to his overnight tally to finish with 5-58 as Pakistan 'A' lost their last wicket with the addition of just two runs.
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