City started brightly and took the lead in the 10th minute when Sergio Aguero swept home his 12th Premier League goal of the season from Aleksandar Kolarov's cross.
Dani Osvaldo responded for Saints with a terrific finish before the interval, and both sides had to settle for a point despite chances at either end in the second half.
While the result could see City fall further off the pace in the title race if leaders Arsenal beat Everton on Sunday, Pellegrini had no complaints after the final whistle as he paid tribute to Southampton's efforts.
"I think it is a good point for us because we didn't play better than Southampton," he told Sky Sports.
"Southampton played very well also. I think it was a very close game for both teams.
"We had one or two other chances and so did they to score, so I think it was a very logical result."
Asked about the difficulty of facing such a hard-working Southampton side, Pellegrini added: "I think we started very well but then we started losing the ball too easily.
"With the players Southampton have in the middle it is really difficult to play when you are always running behind the ball.
"I think it was a really tough game for our team. All of us want to win all the games but today we played against a really good team."