Veteran batsman Ed Joyce was lbw to Mohammad Abbas for four before fellow opener Andrew Balbirnie, who might have been run out for a duck, was lbw to the paceman for nought.
Abbas had lunch figures of two for four in three overs and Amir one for one in 3.1 overs.
Earlier, Pakistan went past 300 after resuming on their overnight 268 for six in a match where Friday's scheduled opening day was washed out completely.
Test debutant Faheem Ashraf top scored with 83 and together with Shadab Khan (55) put on 117 for the seventh wicket.
Middlesex paceman Tim Murtagh led Ireland's attack with four wickets for 55 runs from 25 overs.
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