The 37-year-old offered a frank assessment of a difficult campaign after seeing the Teessiders secure their Barclays Premier League status with Saturday's 2-0 home victory over Portsmouth.
That win - Boro's first in six matches and only their second in the last 11 league fixtures - left them in 14th place in the table on 39 points with one game to pay, two positions and seven points shy of last season's finish.
Southgate's squad has undergone significant change in the last 12 months - strikers Mark Viduka and Ayegbeni Yakubu both left that summer and Jonathan Woodgate followed in January, while Mido, Jeremie Aliadiere, Tuncay Sanli, Luke Young, Gary O'Neil and Afonso Alves have been drafted in at great expense.
The transition, compounded by a series of injuries, has made for a tough season, but he is convinced both he and his players will be better for what they have all gone through.
He said: "There are a lot of things I would have done differently, but I think that would go for every manager in the league and every club in the league.
"Everybody makes mistakes in terms of their decision-making, whether it is in pre-season or during matches.
"The only thing I can say about the group of people we have got here is we are honest in looking at ourselves, we work all the hours that are sent to put things right and we will all be stronger for the experience we have been through this season."
Southgate, whose side entertain Manchester City on Sunday looking to finish with successive wins, will then face a series of tough decisions as he continues his rebuilding programme.
Brazilian midfielder Fabio Rochemback seems certain to leave, while former skipper George Boateng has admitted he could be forced to look elsewhere for regular football and goalkeeper Mark Schwarzer's contract expires in the summer.
However, the former England defender is happy to have tied up some of the club's emerging stars in long-term contracts with David Wheater and Stewart Downing leading the way.
Downing in particular has produced some of his best form yet for the club since signing a new five-year deal to end speculation that he could leave his home-town club.
The 23-year-old has eight goals to his name so far this season and his tied with Tuncay, who drew level with his 53rd-minute strike against Pompey, in the leading scorer stakes.
Southgate, who played alongside Downing during the latter stages of his career, has admitted in the past that the midfielder perhaps did not know how good he could be.
However, he is confident he is now fulfilling his potential and has become a key member of the side.
Southgate added: "Stewart has been outstanding throughout the year. He's gone on to another level in terms of his performances.
"He is delivering away from home as well now, which hasn't always been the case in my time here.
"He has eight goals from midfield, which is a good return for a wide player, and he works his socks off for the team."