Spurs were unimpressive, with Jan Vertonghen missing their best chance from close range in the first half.
Mourinho, who was booked late on, sees his team stay sixth in the table, while Southampton rise to 11th.
Spurs striker Harry Kane was forced off with a leg injury just seconds after having a goal disallowed for offside in the second half.
Shane Long went close with a header with five minutes left, but Southampton are now unbeaten in their last four outings.
Southampton claimed a penalty against Alderweireld for handball early in the second half, but the referee did not give it and VAR upheld the decision, then also upheld the official’s decision against Kane when he netted later on.
Mourinho was shown a yellow card by referee Mike Dean after appearing to go over to speak to members of the Southampton coaching team.
