John Kane, a full-time carer for his disabled partner, was announced as the new councillor for the area just after midnight.
Labour won 43% of the vote in a ward which takes in the constituencies of SNP deputy leader Nicola Sturgeon, Scottish Labour Party leader Johann Lamont and Scottish Labour deputy leader Anas Sarwar.
Mr Kane, who has lived in Govan for 25 years, beat off the SNP’s Helen Walker by a substantial majority.
The by-election followed the recent death of former SNP group leader Allison Hunter. Govan is now the only ward on the council which has no SNP representative.
In the past, Labour suffered two historic parliamentary defeats in Govan to the SNP.
Labour group leader Gordon Matheson said: “There’s no way the SNP can spin their way out of this dramatic result.
“What odds would the bookies have given a year ago on the Govan ward being SNP free?
“With less than 12 months until the referendum, support for the nationalists has slumped in Glasgow.”
Mr Kane said: “This has been a long campaign but the people of my community clearly responded to Labour’s positive message and our plans to bin the bedroom tax, freeze fuel bills and put schools and hospitals first.”
Mr Sarwar claimed the election result would be “devastating” for Ms Sturgeon. He said: This isn’t just in her back yard, its her front room.
“By ensuring the SNP has no representation in Govan in the council, the people of this area have sent Nicola Sturgeon and the nationalists a strong message –stop obsessing about separation and start putting the interests of the people of Scotland first.”
Labour secured 2,055 first-preference votes compared with 1,424 for the SNP candidate.