Zabaleta had been furious after O'Brien's late challenge in the second half, with both players cautioned for their involvement, and the Argentine was immediately apologetic for his role.
"I think it was a bad tackle," Zabaleta told Sky Sports. "I have to say sorry for my reaction, I know it's not the best reaction. I said that to the referee.
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City's vice-captain was full of praise for his team-mates after their win, which came just days after their 3-1 loss away to Tottenham and Manchester United securing the Premier League title.
"For us to come back stronger today was very good," he added. "I think we controlled the game for 90 minutes.
"We were disappointed to concede that goal right at the end, as we should have defended better. But, we have four games until the end of the season, so will need to keep going and we need to try to finish in second.
"We have been working well and we know how difficult it is to win the title. The Premier League is one of the most competitive leagues in the world.
"We've been a bit inconsistent this year, unlike last season, and that’s probably cost us the title. We are working to improve our game year-on-year and looking to win trophies.
"We've got the FA Cup final at Wembley, and it's always special to win that competition as well. We'll try to come back stronger next year and try to win the title back."