Iftikhar took 4-59 to foil a fighting 122 by Chris Gayle as the West Indies, chasing 274 to win, were bowled out for 242 in 46.3 overs to give Pakistan a 3-0 win at the Sheikh Zayed Stadium.
Pakistan won the first match by four wickets and the second by 24 runs.
Gayle fought a lone battle in the lost cause, hitting his second century in the series, but other than him only Ramnaresh Sarwan (62) put up any resistance as Pakistani bowlers led by Iftikhar exploited the conditions well.
The 27-year-old Iftikhar broke the Gayle-Sarwan second-wicket stand of 151 to revive Pakistan's chances, trapping Sarwan in the 33rd over and then dismissing Shivnarine Chanderpaul (three) and Xavier Marshall (nought) in his next.
Gayle, who hit 113 in the first match, was lucky to reach his 18th one-day hundred after television replays showed he edged one from Iftikhar to wicket-keeper Kamran Akmal on 99 but was ruled not out.
Gayle finally fell in the 44th over, caught behind off Umer Gul to end any hopes of an unlikely win. He hit six sixes and five boundaries during his 137-ball knock. Gul finished with 3-31.
Iftikhar's previous best figures of 3-33 came against South Africa at Faisalabad last year.
Earlier Pakistan were helped to 273-6 in their 50 overs by a brilliant 101 by Younus Khan and an unbeaten 79 by Misbahul Haq who together added 103 for the third wicket.
Younus hit five boundaries and a six, and also added 85 for the second wicket with opener Khurrum Manzoor (30) after Pakistan won the toss and batted. Younus and Manzoor steadied the innings after Pakistan lost Salman Butt for nought.
Younus reached his sixth one-day hundred with a sharp single off Daren Powell but two balls later he attempted a reverse sweep off spinner Nikita Miller and was bowled.
Captain Shoaib Malik made 13 and Shahid Afridi managed just six.
Haq continued his good work, hitting three boundaries and a six and added an invaluable 40 for the sixth wicket with Akmal who was bowled off the final delivery for 21.
Pakistan kept an unchanged side, meaning paceman Shoaib Akhtar missed all three matches due to calf muscle injury. West Indies brought in Brendan Nash in place of Carlton Baugh.