Efforts either side of half-time were enough for Gillingham to end the season on a high, putting together a four-match unbeaten run as they just missed out on a play-off place.
Morecambe ended the campaign without a win in their last six games after drawing a blank in Kent.
Danny Kedwell had a shot headed off the goalline by Shrimps striker Jordan Burrow before Lee put the Gills ahead in the 18th minute with a low effort from 20-yards.
Morecambe had goalkeeper Barry Roche to thank for the deficit not being any wider before half-time, the club captain superbly denying Jo Kuffour from point-blank range with the whistle looming.
But Roche could do nothing as Lee doubled his and Gillingham's tally with his sixth of the season 15 minutes from time, sliding the ball home following a clever through ball from Danny Jackman to put the result beyond doubt.