Snape is a very intelligent and resourceful character. In the fan fiction, he could have enlisted the help of some of his allies in the wizarding world. For example, he might have asked a friendly house - elf to create some chaos in Vernon's house. While Vernon is distracted by the chaos, Snape can easily find Harry and take him to a safe place. Also, Snape may have used some potions to make Vernon temporarily incapacitated so that he can't harm Harry.
In this fan fiction scenario, Snape might use his knowledge of the Muggle world and Vernon's weaknesses. Snape could have found out some information about Vernon's business affairs or personal secrets. Then he blackmails Vernon into leaving Harry alone. By doing this, he effectively saves Harry from Vernon without having to use too much magic and draw unwanted attention.
In this type of fanfiction, Snape could simply intimidate Vernon. Snape has an air of mystery and a certain power about him. He might show up at Vernon's doorstep, give Vernon a cold stare, and with his reputation as a powerful wizard, Vernon might be too scared to oppose him. Snape could then just take Harry without much resistance from Vernon.
Perhaps Dudley finally stands up to his father's cruel treatment of Harry. Maybe he realizes that Vernon's behavior towards Harry is wrong and uses his own physical strength or some clever ruse to get Harry out of a difficult situation Vernon has put him in.
It could be that Snape wants to spite Vernon. Vernon represents everything that Snape despises about Muggles who are cruel and unaccepting. By saving Harry from Vernon, Snape is showing his superiority over Vernon and also his power as a wizard. And of course, there's still that underlying reason of his love for Lily which makes him want to protect her son.
Another possibility is that Snape uses his position as a teacher. He might threaten Lockhart with the consequences of harming a student. Given Snape's intimidating presence and his own power within the school, Lockhart would be afraid to cross him. Snape could also call for other teachers to help, making it clear that he won't let Lockhart get away with any harm to Harry.
Well, perhaps Snape could use his authority as a teacher. He might see Ron being too pushy or possessive towards Harry in a romantic sense and intervene by giving Ron extra assignments or detentions to keep him away from Harry.
Snape might do it out of his love for Lily. Since Harry is Lily's son, he feels a sense of obligation to protect him.
Maybe Voldemort uses his magic to stun Vernon first. Then he could simply apparate with Harry to a safe place.
In the fanfic, Snape might use his knowledge of the Dursleys' house layout. He may enter the house unnoticed, find Harry, and then use a Portkey to quickly get them both out of there. He could also have some sort of charm or potion that he uses to counter any magic the Dursleys might have used to keep Harry there, like a spell - breaking potion. And he may have planned the whole rescue very carefully, choosing a time when the Dursleys are least likely to notice, like in the middle of the night.
Perhaps Snape uses magic to create a distraction at the Dursleys' place. He could make strange noises or apparitions that scare the Dursleys, and while they are in a panic, he grabs Harry and disapparates. This would be a quick and efficient way for him to rescue Harry.
Well, he could use his magic skills secretly. Maybe he casts a spell on the Dursleys to make them docile or distracted long enough to get Harry out. For example, he might use a Confundus Charm on them so they don't notice Harry leaving.