In a quiet, stop-start opening the first clear chance of the match did not arrive until the 17th minute when Moustapha Diallo came close to putting the visitors in front by meeting Nicolas Benezet's set piece, but the midfielder could only head wide.
Apart from that opening, both sides were restricted to long-range efforts in a dull first 45 minutes, but the game sparked into life after half time.
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Yannis Salibur fired narrowly wide for Guingamp on the hour mark, but just two minutes later they were behind when Julien Feret ran through the visitors defence and smashed home the game's opening goal.
Guingamp had lost only one of their last nine, but they found themselves 2-0 down with less than 20 minutes remaining as Andy Delort hit a fine second, cutting inside from the left and beating two defenders before firing past Jonas Lossl.
Dorian Leveque's late consolation had Caen sweating, but they held on for a fifth home win from seven matches this season.