Alonso is likely to face retrospective action after stamping on Long's calf in the first half at St Mary's.
Relegation-battlers Southampton took a shock 2-0 lead before the reigning Premier League champions mounted an impressive comeback.
Hughes said: "It's the key moments in games where you just need to be a bit resolute, when you've just got to clear your head a little bit more quickly and get something out of games that you deserve to get something out of".
Should Southampton hold on for the win, it will be enough to take them out of the relegation zone (for the time being at least) in what has been a very tough campaign for the club.
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'I've got a group fighting to get out of this situation but we've not taken points where we should've done again. It could've broken his leg.
"There were three officials within five to 10 yards so how each of them missed it is a mystery to me". Not like him to miss a chance to put himself in the spotlight. "Sometimes you have to have the ability, some would say it's a skill, to knock people over in the right..."
These two however, appeared far more deliberate and intending to cause the opponent injury which is why the offender should be punished and the fact that can't be treated the same on review shows the importance of the referee on the day detecting and punishing them correctly.
Alonso added: "We have to keep giving everything until the end of the season". We will come back stronger for sure.