Life away from the Etihad Stadium has been tough for City, who have won just two away Barclays Premier League matches this season - the latest of which came at West Brom on Wednesday.
It had looked like Pellegrini would oversee another as City came flying out of the blocks on the south coast, with Sergio Aguero sweeping home early on.
However, Saints rallied with a performance that belied their recent poor form and deservedly levelled just before the break through Dani Osvaldo's exquisite strike.
Mauricio Pochettino's side bossed the remainder of the match but were unable to find a winner.
"It is a good point," Pellegrini said. "I don't feel like we lost two points.
"In all the other games away I felt like we deserved more but here this was the result that both teams deserved.
"I always say that if you don't play well and you can't win, then at least don't lose. We didn't play well but we got a point."
It had looked early on as if City would run amok at St Mary's, as Aguero struck home and Aleksandar Kolarov nodded just wide moments later.
Aguero also wasted a gilt-edged chance midway through the first half - something City were made to rue as Southampton's high pressing and possession game made life difficult.
"I know how (Mauricio) Pochettino likes his teams to play and they did very well," Pellegrini said, having faced the former Espanyol boss during the pair's time in Spain.
"It's a hard place to come. It's a very good team, in a good position in the table.
"They lost their last few games against Arsenal, Chelsea and Aston Villa but before that they played really well.
"We lost control of the game. We started well, we had chances to score the second one and after that I think we started to play too quickly. That was the problem during the first half."
Much will be made of another underwhelming away display by City, but Southampton deserve credit for their performance in the face of adversity.
Successive losses to Arsenal, Chelsea and Aston Villa have been compounded by mounting injury worries, with seven first-team players unavailable for this match.
"I think overall the performance was amazing from my team," Pochettino said.
"I think we have been on a negative run of results as of late but the thing about this team is it keeps believing.
"I think this bad run of results we have been on has been due to different factors - maybe we have been unfortunate a little bit in a few of these games.
"This team believes and I think this team is on a good run in how it plays. It tries to play always the same way, it tries to play well the same way.
"I think against Manchester City we beat them on possession against a team that has the biggest record on possession in the league. Overall I am very happy with the team."
One player in particular, though, will undoubtedly take the headlines.
Osvaldo put City captain Vincent Kompany on his backside, cut back past Pablo Zabaleta and shot into the top corner to draw Saints level in style.
"It was a great goal," Pochettino said of the man wh0 may well face England at next year's World Cup with Italy.
"I think we were all able to see it and to all eyes it was an amazing goal."