Chasing a modest 263 for victory, Afghanistan's opening batsmen Mohammad Shahzad and Hazratullah Zazai got them off to a blistering start before Shahidi took charge to help them cross the finish line in the final over.
"It's a great victory for the people of Afghanistan," skipper Gulbadin Naib said. "If you look at Pakistan, it's one of the best sides. You can't take anyone easily. At the World Cup anything can happen, so we will do our best."
Pakistan batsman Babar Azam, who shone in their 4-0 series defeat by England this month, continued his excellent form with the bat ahead of the World Cup by scoring 112 off 108 balls but his team were restricted to a below-par 262 in 47.5 overs.
Afghanistan spinners Mohammad Nabi (3-46) and Rashid Khan (2-27) then choked the Pakistan batsmen to lay the foundation for a famous win while pacer Dawlat Zadran claimed two wickets, including that of the dangerous Azam.
"Not enough runs on the board. (We were) 15-20 runs short and we didn't start well with the ball, that's why we lost," Pakistan skipper Sarfaraz Ahmed said.
"It's very tough if we're losing matches. I tell my boys to back themselves... we'll do well soon. Our batsmen are in good nick... but we need to work on our bowling."
Zazai attacked the Pakistan bowlers after opening partner Shahzad retired hurt on 23 with a left knee problem. The 21-year-old smashed eight fours and two sixes in his 28-ball 49 before being caught at mid-wicket off Shadab Khan's bowling.
Shahidi then anchorws the innings to perfection with a patient knock that included seven boundaries to secure a famous victory.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Toby Davis and Ken Ferris)
