First-half goals from Jay Rodriguez and Rickie Lambert handed Mauricio Pochettino another prized scalp, with Chelsea briefly drawing level courtesy of a John Terry header.
The Blues have now lost three successive away games in the league and dropped below Tottenham into fourth place, with fellow London rivals Arsenal just two points adrift in fifth.
Despite the result Benitez, who was again the victim of jeers and negative chanting from the travelling Chelsea support, reckons no-one will be certain of a Champions League position until the very end of the campaign.
"It is the same situation, if we had three points more it would be easier," he said. "We still have one game in hand and we have to carry on and concentrate and move on and start thinking about Monday (FA Cup quarter-final replay v Manchester United).
"In the league you still have a lot of games and I think it [the battle for a top-four finish] will run for the rest of the season."
This was Chelsea's first game in a run of six matches in a 16-day period and Benitez made no fewer than seven changes from the team that won against West Ham before the international break.
The former Liverpool boss said the fixture pile-up is something the Football Association needs to "look at" in the future but did not regret rotating his players.
"We had to manage the squad," he said. "We didn't have many options in some positions so we had the players we had to use. You have to approach every game like it is the most important and we thought with these players we would be fine.
"I think that you could see that in the first half we didn't have the intensity we were expecting.
"We improved in the second half, made more chances, but still we didn't make the right decisions in the final third but at least we were there and made the chances."
Pochettino, who has now won three, drawn three and lost three games since replacing Nigel Adkins as Saints manager in January was quick to defend his Chelsea counterpart following the game.
"I have a lot of sympathy [for Benitez's position]," he said.
"I fully recognise the job that he has done.
"For me he is one of the best managers in the world and he has my full respect for what he has achieved in football."
The win against Chelsea follows earlier home successes against Manchester City and Liverpool and Pochettino believes beating some of the league's biggest names can only boost the morale around the club.
"Victories like those of today prove that we are on the right path," he said.
"It is very important for the confidence of my players and especially the people surrounding our club - the technical staff.
"It is important that we believe we can achieve results as we saw today and we can continue achieving them in the future."