Pellegrini's free-scoring team appeared in ominous mood early on and Sergio Aguero scored his 18th goal in as many starts this term to hand them a 10th-minute lead.
But Mauricio Pochettino's injury-hit side responded with a display of endeavour and quality and were rewarded with a magnificent 42nd-minute equaliser from Pablo Daniel Osvaldo.
"The result, I think is a good point for us because we didn't play better than Southampton," Pellegrini told Sky Sports.
"Southampton played very well and I thought it was a close game for both teams.
"We had one or two options (chances) more and so did they so I think that was a logical result, seeing over the 90 minutes what both teams did."
City have now won only two of eight Premier League away games this season in stark contrast to their perfect seven-game home record.
They took their swashbuckling Etihad Stadium form on the road to beat West Brom on Wednesday but Saturday's display once again demonstrated frailties that threaten to derail their Premier League title bid.
Most notably, Southampton's three-man midfield of James Ward-Prowse, Jack Cork and Steven Davis overwhelmed Yaya Toure and Fernandinho in the City engine room for a sustained period, forcing Pellegrini into a re-think after 62 minutes when holding player Javi Garcia replaced striker Alvaro Negredo.
But the former Villarreal and Real Madrid manager pointed the blame at poor ball retention rather than his persistence with an expansive 4-4-2 approach both home and away.
"I think that we started very well but after that we lost the ball too easily," he added.
"When you play against a team like Southampton in the middle it is very difficult when you are always running behind the ball.
"They were a very tough team and it was a very tough game for our team. All of us want to win all the games but today we played a very good team."
