Team management said Junaid suffered a toe injury on his right foot and will be out of the series.
Later, the Pakistan Cricket Board confirmed on Twitter that Imam's scans were clear.
Shaheen's 4-38 kept New Zealand down to 209-9 in their 50 overs before Zaman returned to form with a run-a-ball 88 for his seventh fifty to guide Pakistan to their target for the loss of four wickets in 40.3 overs.
The visitors were in a precarious situation at 73-4 but a 75-run stand for the fifth wicket between Ross Taylor and Henry Nicholls averted the risk of being dismissed for a low total.
In the first Pak Vs NZ encounter, green shirts lost the match by 47 runs. The win also sets up an intriguing final match in Dubai on Sunday. We hoped to come back strongly and we did, ' revealed Pakistan skipper Sarfraz Ahmed after the match.
Kim & Kourtney Kardashian Evacuated After Woolsey Fire Hits Calabasas
At 2:30 am her sister Khloe tweeted out "I cannot sleep! I am too nervous with these fires #MamaKoKo", Khloe posted on Twitter . Kim quote tweeted it with a number of prayer emojis before her property was affected. "I need an evacuation update please".
Captain Kane Williamson, who won the toss and elected to bat, was unlucky to get run out when Afridi got finger tips off George Worker's hard drive and the ball smashed onto the stumps at the non-striker's end with Williamson out of his crease. "It wasn't enough on that surface".
Owen Farrell got away with a controversial tackle on Andre Esterhuizen beyond the 80th minute in a 12-11 victory over South Africa last weekend, but Eddie Jones' side saw a marginal call go against them on this occasion as Sam Underhill's 75th-minute try was controversially chalked off by TMO Marius Jonker.
Undeterred by Imam's injury, Zaman added a quick 101 for the second wicket with Babar Azam who made a 50-ball 46 before both fell in the same Ferguson over. The spin trio of Mohammad Hafeez, Shadab Khan and Imad Wasim displayed so much control for there was just one boundary hit in their collective 25 overs.
Fakhar Zaman smashed run-a-ball 88 and fast bowler Shaheen Afridi (4-38) grabbed his second successive four-wicket haul in Pakistan's six-wicket victory against New Zealand in the second one-day global (ODI) on Friday.
Neither George Worker (28 off 50 balls) nor Henry Nicholls (33 off 63) looked particularly at ease in their time at the crease, but both batsmen were also put in hard situations as failures from Colin Munro (13) and the duo of Williamson and Tom Latham (one run apiece) put the Black Caps in early strife. Taylor hit three boundaries and a six for his 43rd half century in one-day internationals.