Late in the first half, with Southampton winning 1-0, Alonso appeared to go in high and catch Southampton forward Shane Long’s leg with his studs.
While Long was able to continue, the tackle easily could have been a straight red card, but referee Mike Dean did not issue any punishment to Alonso for the incident.
The Blues eventually came from 2-0 down to claim the three points, with relegation-threatened Southampton's misery being compounded by the fact Alonso assisted the Chelsea opener.
However, speaking after the match, Conte refused to comment on the tackle itself, claiming he did not see the incident.
“I must be honest, I didn't see this,” Conte said. “We have never commented about the negative refereeing decisions, especially after the game. This is because it is difficult to watch the game images but I think in the past I have never complained about a negative situation for my team.
“I have the same behaviour for this also, because I didn't see it and I can't comment.”
However, Conte's opposite number Mark Hughes was unhappy that Alonso had escaped a red card and has called for the player to receive a retrospective ban ahead of next week's FA Cup semi-final between the two clubs.
The Southampton boss said: "It was a poor challenge, a really poor challenge. It should have been a red card, clearly. I am disappointed that the officials didn't see it. They were all within a 10 or 15 metre radius. I think between the referee, linesman or fourth official that one of them should have seen it.
"It was a poor tackle, it was a tackle that thankfully had no drastic consequences for Shane. Thankfully he is okay, he just got a rake down the calf. Clearly, with Chelsea down to 10 men and us in the first half on the ascendancy, it is a slant on the game really.
"Those are key moments and referees have got to get them right, maybe that's why the [Premier League] referees are not at the World Cup this year."
Meanwhile, Conte did have words for his side’s poor performance for the first 60 minutes of the contest, which saw the Blues fall 2-0 behind following goals by Dusan Tadic and Jan Bednarek.
However, he also credited their recovery, as Olivier Giroud’s brace sandwiched a goal from Eden Hazard to complete the comeback and secure Chelsea three points to keep them in the hunt for the top four.
"The first half wasn't good, not only from a tactical aspect," Conte told Sky Sports. "I think we didn't show great spirit, great desire, great fight for a good result.
"Don't forget we went 2-0 down, but we had the right spirit to come back and win the game. If you don't have something in your heart, it's very difficult to come back and win.
"I'm very disappointed for the first half, and I'm the first to take fault for it, but in the second my players deserve credit.
"In every game we must play with great passion, spirit. You can lose, draw or win, but in your mind and heart you must know you have given everything for this team, for this colour for our fans.
"This the most important thing and we must finish the season with this spirit."