Referee Jones booked City striker Aguero for diving at St Mary's on Sunday, despite the Argentina hitman being clearly upended by Jose Fonte.
Jones produced a mixed display at best, also bringing back play for a Saints offside offence despite City defender Eliaquim Mangala launching a dangerous attack.
Southampton were also left frustrated by a yellow card for Victor Wanyama's tackle on Yaya Toure, where the hosts felt the Kenya midfielder took the ball.
Now Professional Game Match Officials Limited (PGMOL), the governing body of top-flight referees, have handed him an off-pitch role for next weekend
Jones' next assignment is the match between West Brom and West Ham on Tuesday night - an assignment made before Sunday's display.
City cruised to victory over Southampton on Sunday thanks to goals from Yaya Toure, Frank Lampard and Gael Clichy, but Jones' controversial penalty call came early on with the score still 0-0.
Fonte felled Aguero in the area and was fortunate to escape at least a yellow card for his challenge.
Both City boss Manuel Pellegrini and Saints manager Ronald Koeman said Jones should have awarded a penalty, but also sympathised with the tough job facing referees.
Jones sent Mangala off for two bookable offences, though that decision was deemed correct by City manager Pellegrini.
"I saw that it was a penalty but I am not the referee," said Pellegrini on Sunday.
"Sergio never dived, but the referee is human and everyone makes mistakes.
"Maybe if we had drawn 0-0 we would be talking more about this, but we got the result and that's all that counts."
Southampton boss Koeman hinted that Jones had perhaps denied City a penalty in trying to even out the early decisions after handing Wanyama that questionable yellow card.
"Maybe it was a penalty, but I think the reason that the referee didn't give that penalty was that he understands after giving a foul against Wanyama that he had played the ball," said Koeman.
"That was a mistake, and maybe (not giving a penalty) that was his second mistake.
"That's like in the beginning a little bit to try to keep it in balance for both teams."
Source : PA
Source: PA