The game started brightly with both sides creating enough decent chances to take the lead.
Darius Henderson and Jonathon Douglas kept Crewe's Clayton Ince busy throughout the game with numerous stinging drives.
Steve Jones was the pick of the Crewe strikers and he could have had a hat-trick on another day, but the Northern Ireland international limped off at half time with a hamstring injury and was replaced.
Jones was at the heart of all of Crewe's best moves, setting up Neil Sorvel who shot wide after 20 minutes.
And when his own shot was saved well by the legs of Jason Brown, Luke Varney hit the crossbar just minutes later when trying covert the rebound.
Ince pulled off the save of the match with just 27 minutes left when second-half substitute Matthew Jarvis whipped in a delightful cross and Henderson powerfully headed the ball goalwards from just 12 yards only to be denied by the Trinidad & Tobago international
David Vaughan looked to have given Crewe their first win since New Year's Day with a measured 20-yard drive leaving Brown no chance.
Gillingham were stung in to action and were soon back on level terms when Southall scored his first goal of the season on 80 minutes to stretch their unbeaten run to nine games.
The home side rallied late on and Vaughan cleared Henderson's shot off the line with the last kick of the game.