The English Football Association confirmed the Chelsea forward was left out of Sunday's 3-0 win over Senegal to deal with "a family matter".
The England attacking midfielder posted an emotional message on social media, along with a video of highlights of his time at City.
Sterling has scored 20 goals for club and country this season, which includes a 13-minute hat-trick against Watford.
England fan Ife Runtwe reflected on his team's five-star first half against Panama, calling it the 'est England experience he had in his life.
A spat between the England camp and the British media erupted earlier this week after photographs apparently showed Southgate's assistant carrying the team selection for Sunday's Group G clash.
Sterling's father was shot dead in his birthplace of Jamaica when he was just two years old.
Sterling hasn't scored in his last 20 games for England, stretching back to 2015.
Southgate claims Sterling justified his decision to protect the troubled England star despite his booking for diving against Nigeria.
Southgate's side swept into a two-goal lead as Gary Cahill and captain Harry Kane netted in a dominant first-half display at Wembley.
England boss Southgate has made it clear he demands the highest professional standards and the 23-year-old got the message that he had to take his England commitments seriously.
Brazil international Jesus has not featured for the Premier League leaders since he suffered a knee ligament injury against Crystal Palace on December 31.
Raheem Sterling side-footed wide in front of an open goal in the second half when City was leading through Danilo's strike on Saturday.
Tunisia will meet England in their first game in World Cup Group G, which also contains Belgium and Panama.
A slew of statistical milestones have littered red-hot City's incredible run and they can finish 2017 by claiming another notable feat.
Guardiola refused to be drawn into a war of words with Mourinho after Manchester City maintained their impressive run.
Guardiola's side moved 15 points clear of second placed Manchester United thanks to Raheem Sterling's first half strike.
Sterling's 31st minute goal ensured Manchester City took advantage of second-placed Manchester United's costly draw with Burnley.
Manchester City became the first EPL club to score over 100 goals in a calendar year since Liverpool achieved the feat in 1982.
The court was shown CCTV of the accused, Anderson, who has a history of football-related violence, driving his van alongside Sterling's vehicle as the player waited to enter the training ground.
When Manchester City forward Sterling got out of his car, the man is alleged to have kicked him and shouted racist abuse.