Stand-in skipper Shadab Khan gave an allround performance to guide Pakistan to a consolation 66-run win in the third and final Twenty20 international in Sharjah on Monday but Afghanistan take the series 2-1.
Having lost the first two match by six and seven wickets respectively, Pakistan's new-look side posted a strong 182-7 in 20 overs before restricting Afghanistan to 116 in 18.4 overs.
Opener Saim Ayub led an improved batting show as Pakistan scored 182-7 after their below-par 92-9 and 130-6 in the first two matches.
Shadab then became the first Pakistani and seventh bowler overall to complete 100 T20I wickets in his 87th match, claiming 3-13.
Afghanistan were never in hunt for the stiff target as fiery pacer Ihsanullah dismissed Rahmanullah Gurbaz (18) and Karim Janat (nought) before his sharp bouncer left Najibullah Zadran's chin bleeding.
Najibullah was stable but could not resume his innings. Azmatullah Omarzai, concussion substitute for Najibullah, top-scored with 20-ball 21, hitting a six and two boundaries. Ihsanullah finished with 3-29.
Mohammad Nabi was run out for 17, Rashid Khan made 16 and Usman Ghani scored 15 before becoming Shadab's 100th T20I wicket.
New Zealand's pacer Tim Southee leads the T20I wicket takers with 134 followed by Bangladesh's Shakib Al Hasan (131), Afghanistan's Rashid (129), New Zealand's Ish Sodhi (114), Sri Lankan Lasith Malinga (107) and Bangladesh's Mustafizur Rahman (100).
Despite the series defeat, Pakistan can take heart from the fact that they checked their bench strength, having rested regular skipper Babar Azam, Mohammad Rizwan, Fakhar Zaman, Shaheen Shah Afridi and Haris Rauf.
Shadab said the motive for the series was achieved.
"The main motive of this series was to give the youngsters a chance, hopefully, they will get confidence from these matches and it will help them in the long run," said Shadab.
Series win, Rashid said, was memorable.
"It's special to be part of this team, it was a great effort from everyone. We won the series, but we have some areas to improve on," said Rashid.
"Any series after this is a good preparation for us before the World Cup," said Rashid of the 50-over World Cup in India later this year.
Earlier, Ayub hit a solid 40-ball 49 with two sixes and four boundaries while Iftikhar Ahmed scored 31 from 25 balls with two sixes.
Shadab, who made 28, and Abdullah Shafique (23) were the other main run getters.
For Afghanistan spinner Mujeeb Ur Rahman was the pick of the bowlers with 2-28.
Afghanistan won the first match by six wickets and the second by seven, also in Sharjah.
The series was arranged in replacement for three ODI matches which Afghanistan were slated to play against Australia this month in the United Arab Emirates.
But Cricket Australia abandoned the series in protest of Afghanistan's ruling Taliban putting a ban on women's education and cricket in their country.