The party took legal action against the Electoral Commission over what it said was the refusal to allow the slogan “Anas Sarwar – Labour’s National Recovery Plan” to be on regional list ballots for the May 6 poll.
Earlier this month, Labour applied to have a description featuring its Scottish leader’s name and an election slogan featured on ballot papers.
But last week the Electoral Commission said it could not deal with the application in time for the description to be included on ballots.
At a remote High Court hearing on Tuesday, Labour said refusing to include the slogan on regional list ballots would cause it “an unfair electoral disadvantage”.
The party argued it would face “a situation where other parties, but not it, can use ballot paper descriptions that refer to their current leaders and/or up-to-date campaign straplines”.
But the Electoral Commission said all applications to register a description had to be “considered by the Electoral Commission’s internal approval board and published for public consultation” before they could be determined.
It also said Labour made its application “very late” and the party should not be “pushed up the queue” ahead of other applicants.
In a ruling on Wednesday, Mrs Justice Ellenbogen refused to grant Labour an order requiring the Electoral Commission to make a decision on its application before the deadline for delivering nominations later the same day.
The judge said doing so would cause prejudice to “other applicants, the electorate and the defendant’s independence from political pressure”.
She ruled the Electoral Commission had not refused Labour’s application, but that its response had simply been to follow “its standard process”.
The judge also rejected Labour’s contention that it would be caused “substantial prejudice” by not having Mr Sarwar’s name on the ballot papers.
Mrs Justice Ellenbogen said Labour’s campaign “messaging, together with Mr Sarwar’s high profile in Scotland” meant any prejudice to the party would be “substantially less significant than has been asserted”.
She also ordered Labour to pay the Electoral Commission’s legal fees of just over £9,000.
A Scottish Labour spokesman said: “We took this action to ensure we were represented appropriately on the ballot paper in this election and are disappointed with this ruling, which failed to recognise that Anas has only been leader for one month.
"However, recovery is very much on the ballot in May and only a Labour vote will deliver the national recovery plan that Scotland deserves."