Opening batsman Paul Stirling scored 76 off 43 balls and the 39-year-old Johnston hit a rapid 62 off 32 with five fours and four sixes in Ireland's strong total of 225-7 after it won the toss and elected to bat.
Medium fast Johnston - who will quit international cricket at the end of the year - took 3-34 with the ball, including Afghanistan top scorer Gulbadin Naib (43) and Samiullah Shenwari (5) off successive deliveries.
Afghanistan was bowled out for 157 in 18.5 overs.
Nepal finished third in the tournament with a five-wicket victory over United Arab Emirates in the playoffs.
Ireland beat Afghanistan in final to retain ICC World T20 Qualifiers title
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