The top court late Friday ordered the education ministry to delay implementation of the training programme until a ruling is made on a legal challenge to the scheme.
The government has said the three-week residential military training program, which was due to begin on Monday at military camps, was aimed at boosting leadership qualities.
The programme did not involve the use of weapons, the government said.
The petition against the military training, which is to be heard on Monday, called the programme "degrading" for undergraduates and a violation of their constitutional rights.
The government says it has been forced to introduce the "leadership training" in a bid to discourage rampant ragging -- bullying of newcomers by older students -- at Sri Lankan universities despite a 1998 law banning the phenomenon.
Ragging has caused several deaths and many severe injuries among students.
Some 20,000 students a year qualify to enter Sri Lanka's 19 universities and technical colleges run