The 52-year-old named a under-strength line-up with big games in the FA Cup and Europa League on the horizon, but was adamant that the players named were good enough to win
The Spaniard left the likes of Eden Hazard, Ashley Cole and Demba Ba on the bench for the clash at St Mary's, with his side facing an FA Cup quarter-final with Manchester United on Monday before a Europa League quarter-final and another league game in the same week.
But the 52-year-old defended his decision to leave the key men out, suggesting their busy schedule means rotation is necessary and indicating the players picked still had enough ability to win.
"We have to manage the squad," he told reporters. "We don't have so many options in some positions. These players were [good enough to win].
"[Gary] Cahill and [Juan] Mata couldn't play, so it's not a question of whether we were resting these players in this match.
"The first half we didn't have the intensity we were expecting. We improved in the second half and created more chances but we didn't make the right decisions in the final third.
"It could have been different if we did much better in the first half, then we had the chances in the second half to win."
The loss sees the west Londoners drop to fourth in the Premier League table, with Tottenham jumping above them into third and Arsenal moving just two points behind in fifth.
Despite the disappointment, Benitez believes his side are still in a good position to secure Champions League football next season, but it now fully focused on the FA Cup tie with the Red Devils.
"[To get] three points would [make it] easier," he admitted. "But we have one game in hand and have to carry on and concentrate on Monday.
"We cannot waste too much time thinking because we have to be ready for the next challenge. It's another competition, another challenge. If we win we are in the semi-finals. In the league we still have a lot of games and I said it will go to until the end of the season."
Saints boss Mauricio Pochettino, on the other hand, was delighted with his side's display as they added to the list of top-half teams they have defeated this season.
"Victories like those of today confirm we're on the right path," he said via a translator. "It's important for the confidence of my players and the technical staff.
"It's important we can believe we can achieve results like today and continue to in the future."