The Spaniard has made no secret of the fact that he had one eye on Easter Monday's FA Cup quarter-final replay against Manchester United and their forthcoming last-eight matches in the Europa League against Rubin Kazan.
Ashley Cole, Eden Hazard, Ramires, Demba Ba and David Luiz were all relegated to the bench as Benitez made seven changes in all to his starting eleven for the Premier League clash at St Mary's, while Gary Cahill and Juan Mata were missing through injury and illness respectively.
However, the interim manager remains confident that his side will qualify for the Champions League despite relinquishing third place to Spurs yesterday after they beat Swansea.
Chelsea have already played 54 games this season and the former Liverpool boss is convinced that rotation of his squad during the run-in is key to their hopes of success.
Benitez told Sky Sports: "You have to make decisions and use the squad.
"Southampton is a good team on one level and Manchester United is another team on another level.
"In the league, you have more games to play and will be going to the end. In the FA Cup you have one game and you will be out.
"You have to find the balance for players who are playing more games or less games.
"I have confidence that we will finish in the top four and maybe we can win one or two trophies.
"I have the belief and the confidence in these players because they have the quality and if they realise that we have to start games with the same intensity as the second half (against Southampton), we can beat anyone.
"This one is so close. 48 hours, less than 48 hours, you have to make decisions. If you have three days, four days you can manage in a different way. But two days between games is not easy."