Goals from Aaron Ramsey after 50 minutes and Gareth Bale in the 86th, sealed their sixth win of the campaign which has ended with them reaching a major tournament for the first time since the 1958 World Cup finals.
Andorra, who had lost 53 successive competitive matches before this one, frustrated Wales throughout a one-sided match which was played out almost entirely in Andorra's half of the pitch.
Wales had 24 attempts on goal, 11 of them on target, but Andorran goalkeeper Ferran Pol had a good game and saved his side from a much heavier defeat with some accomplished saves, even if he was booked for time-wasting in the second half.
Ramsey scored when he followed up a rebound off Pol, who had parried a header from Ashley Williams, while Bale slammed in from close range after a good run from defender Ben Davies.
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The result means that Belgium, who like Wales, had already qualified for the finals, finish top of the group with 23 points, followed by Wales on 21, with third-placed Bosnia going into the playoffs with 17 points.
Israel, Cyprus and Andorra filled the bottom three positions.
(Writing by Mike Collett; editing by Toby Davis)
