Words were exchanged across the technical area and Jewell later branded the Blues' behaviour as 'unsporting'.
Mourinho hit back by saying Latics had cheated because McCulloch wasn't injured, but went on to express his admiration for how the club has adapted to the Premiership.
The Chelsea boss said: "The comment by Paul is not a correct one and when you lose matches sometimes you have to say something.
"Maybe he brought the attention to this point but he didn't need to do that.
"They (Latics) should have congratulations for their work, they have done brilliantly this season. At the moment they are not getting the points but they are playing against the best teams in the league.
"They are having a fantastic Premiership season, Paul is doing a wonderful job."
The game was goalless when Jewell and Mourinho had their spat, and the incident had no bearing on the outcome.
But Jewell was angry enough about what had gone on to raise the issue at the post-match press conference.
He said: "When we kicked the ball out when one of our players was injured, they kept it which shows they must have feared us. I just thought it was a bit unsporting for Chelsea to do that.
"It upset me a little bit, I thought Jose had told them to give it back to us, but the lads say he told them not to.
"I'm disappointed in that, but I wish it was me being unsporting after getting three points, not them."
Mourinho's response was typically forthright, saying: "It was my responsibility because I told William Gallas not to give the ball back.
"The reason why was because we know what fair play is, I'm not stupid. When the player is injured we give the ball back, when the player is cheating we are not stupid.
"Because the player was cheating – two seconds later he was standing up and running again – I told Gallas not to give it back. I will do it again, fair play is not to cheat.
"This happened two metres in front of me, all my staff were completely sure about it.
"Five minutes later, McCulloch was injured and we kicked the ball back.
"If Paul was angry, he should have told me because he was with me."
Jewell was pleased with Latics' performance, except for the manner in which they conceded the game's only goal.
It took Chelsea until the 67th minute to break them down, skipper John Terry heading home a Frank Lampard corner.
Jewell said: "At one stage I thought we would get a draw out of it, we defended manfully and played a lot better than we have been doing.
"But to concede a goal at a set-play was a double whammy, it was disappointing.
"When Chelsea beat us in the first game of the season, I could take it because it was a wonder goal. But this time it was almost a gimme."
Jewell made four changes to the side, bringing in Matt Jackson, Josip Skoko, Ryan Taylor and David Connolly. He said: "We play a lot of games in a season, have a busy schedule coming up and we haven't the biggest of squads.
"In the past we haven't had the luxury to rotate, but this time I thought some of the lads deserved a chance while one or two looked a bit jaded.
"On Saturday we looked more like a team then we did against Liverpool the week before.
"Defensively we did well, and while we didn't create many chances, not many sides do at Chelsea.
"We are nearing the end of the run of tough games, and out of the four so far, there has only been Liverpool where we didn't look like a decent side."