The winger looked to be heading for the St Mary's exit when he criticised the club's owner Nicola Cortese on Twitter.
Puncheon was immediately disciplined for his actions and was subsequently linked with moves to West Ham United, Middlesbrough and Blackpool.
However, the two parties have now appeared to patch up their differences.
"I admit my mistakes as a grown man, both my actions over the weekend and for the things that have occurred in the past, so I am pleased that Nicola has accepted my apology and granted me a clean slate," Puncheon told the club's official website.
"I know that I have a point to prove, and I know that some supporters have been on my back for the way that I have behaved in the past. I can only put that right through my performances on the pitch and showing that I am committed to Southampton."
Puncheon has not played for the Saints since 2010, having had several loan spells away from the club.