The midfielder started Sunday’s 2-1 defeat at Liverpool, just a week after missing the club’s final pre-season friendly.
Schneiderlin had been allowed to sit out the Bayer Leverkusen match after declaring himself to be neither physically nor mentally prepared to play.
It was a situation that arose after the St Mary’s board informed the Tottenham target he would not be sold this summer.
Despite his disappointment and frustration, Schneiderlin returned to training last week in a good frame of mind, according to manager Ronald Koeman, who added he had “accepted” the club’s decision.
The 24-year-old’s efforts were enough to satisfy Koeman that he should start at Anfield, and team captain Fonte was delighted to have him in the line-up.
“It means everything,” he said. “We all know how important he is.
“He’s a great player and he showed again why there is interest in him. I’m just thankful that he played for us.”
Schneiderlin is understood to believe he had a verbal agreement with the club that he could leave this summer.
However, that was said to have been struck with former chairman Nicola Cortese, meaning it holds no weight with the current board, who understandably wish to retain the player.
Despite the issues that have arisen in the background, Fonte insisted that Schneiderlin has remained a committed member of the squad.
“He’s always been a very good professional,” he said. “He’s always been on top of his game and he does what he has to do. He still has a contract with us and he has been very professional.”
Tottenham have already failed with one £10m offer for Schneiderlin, and there are suggestions they will return with an improved bid.
The Saints board have been consistent in their stance so far, however, that they will not sell the player.
Fonte, who has played in the same side as the Frenchman for the last four-and-a-half years, believes it would be a huge boost to the team if they retain him for the season.
“It would be massive,” said Fonte, who added that he “hopes” Schneiderlin will still be at Saints after the transfer window has shut.
“He’s one of the most important players for us, so we’re just pleased that he’s still with us.”