Babar, Shan Masood and Salman Agha missed 1st session as they were reportedly down with flu.
The skipper, who hit 161 in the first innings, was seen on the field in the last two sessions on Day 2.
With Mohammad Rizwan not picked for this Test match and Sarfaraz Ahmed returning to the side, confusion was whether who was going to lead the Pakistan side in the middle in Babar's absence.
Meanwhile, Rizwan came onto the field as a substitute fielder and began marshaling the troops, setting fields, and talking to bowlers. But the MCC rules state that "a substitute shall not bowl or act as captain but may act as wicket-keeper only with the consent of the umpires.”
However, things became clearer when keeper Sarfaraz Ahmed called for a review and he even got one spot-on when Nauman Ali appealed for LBW against Devon Conway. After consultation with the bowler, the former captain took the review and got the on-field umpire's not-out decision overturned.
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This meant that Sarfaraz, who was making his comeback into the Pakistan team after more than three years was leading the side once more, despite the presence of Rizwan, who was still seen setting the fields.
Apart from Rizwan, Sajid Khan and Kamran Ghulam were also on the field as substitute players with Shan Masood and Salman Ali Agha also down with flu as per reports.
Rizwan managed scores of 29, 46, 10, 30, 19, and 7 in the 3-Test series against England as Pakistan slipped to a 3-0 whitewash in a Test series for the first time at home.
Sarfaraz, meanwhile, hit a brilliant 86 in the first innings and helped Pakistan post 438 runs on the board in the first innings. New Zealand gave a strong response with openers Tom Latham and Conway adding 183 runs. Conway got out for 92, while Tom Latham hit 113 runs.