After beating Salem 2-1 in the semifinals, Myrtle Beach lost Game 1 of the Finals before catching fire and winning three in a row to clinch the club's fourth title.
The Pelicans split a title with Wilmington in 1999 and won the league outright in 2000 and 2015.
Lynchburg, fighting to keep its title hopes alive, got on the board first via Francisco Mejia's (Indians' No. 4, No. 88 overall) RBI double in the bottom of the first.
Eloy Jimenez (Cubs' No. 2, No. 24 overall) tied the game up with a base hit in the third before Myrtle Beach took a 2-1 lead on an error later in the inning.
Mejia gave the Hillcats the lead again with a two-run homer in the bottom of the frame, but Myrtle Beach eventually sealed the deal with a three-run seventh.
Donnie Dewees (Cubs' No. 11) fittingly scored the go-ahead run. Dewees, who hit .284 in 129 games across two levels this season, has been on fire in the postseason. The center fielder hit .423 in six games, recording hits in five of the six contests and went 3-for-5 with a run scored in the decisive game.
Preston Morrison, who posted a 2.11 ERA in 23 games this season, gave up three runs in three innings, but the bullpen was lights-out and sealed the deal. James Pugliese retired the first 13 batters he faced and gave up one hit with seven strikeouts in 4 1/3 innings of relief. Once he was done, Tommy Thorpe and Ryan McNeil pitched the final 1 2/3 frames.
The Pelicans were the second club in the Cubs organization to clinch a Minor League title after the Eugene Emeralds won the Northwest League championship on Tuesday night.
William Boor is a reporter for MLB.com. Follow him on Twitter at @wboor. This story was not subject to the approval of Major League Baseball or its clubs.