The 35-year-old secured a surprise victory in the men's 100m final at IAAF World Championships on Saturday, beating crowd favorite Bolt on his final individual race before retirement.
Gatlin, who has twice been banned for doping offenses, was booed every time he was introduced to the crowd at the London Stadium before the 100m heats, semifinals and final. Spectators again jeered once it was clear that the 2004 Olympic champion had won gold and ruined Bolt's farewell.
The crowd's dissatisfaction was less audible when Gatlin stepped on top of the podium to collect his medal, but some fans did make their displeasure known.
Gatlin is the sport's most controversial drugs cheat. He was banned for two years in 2001 when he was still at college. He served 12 months of his sentence for taking a banned amphetamine after successfully arguing he had taken the drug as medication for attention deficit disorder.
In 2006, he was banned for eight years, later reduced to four on appeal, after testing positive for the banned steroid testosterone.
Asked how he felt about the crowd's reaction in London, Gatlin told CNN: "It leaves me scratching my head.
"I've been back in the sport since 2010. I wasn't booed in 2012, '11, '12 -- which was still in London -- '13 or '14 or '15 and not that much in '16.
"I understand why, you have black hat, white hat; good, evil, but I think it was sensationalized by the media between two people who have the utmost respect for each other."
'A mutual friendship'
Gatlin genuflected to Bolt after the race to show his respect to the most successful sprinter in history, a man many inside the stadium hoped would sign off triumphantly.
Instead Bolt, who has reigned in an era darkened by doping, had to settle for bronze. The Jamaican will now hope to add to his tally of 11 world titles with victory in the men's 4x100m relay.
"At this championship many people saw we do have a mutual friendship," said Gatlin.
Nine of the 30 fastest 100m times, including the top four, are Bolt's. The other 21 marks on that list have been run by athletes who have, at some point, tested positive for doping.
The spotlight fell on Gatlin in particular in 2015, when the American was clocking sensational times throughout the season and went into the World Championships in Beijing on a 28-race unbeaten and looking likely to topple Bolt from his throne.
Three other men in that final had recently returned from doping bans, but it was Gatlin versus Bolt which was characterized by many as good versus evil. A showdown Bolt won by one hundredth of a second.
"I've served my time," added Gatlin.
"I went through all the channels of getting back on the track and that's how society is. You correct yourself in normal society. That's what I've done.
"I've tried to inspire younger athletes what to do, what not to do, and that's what I'm here doing, just trying to be the best person I can be in life."
'Showering with the medal'
Gatlin admitted he had not let the medal out of his sight following his victory.
"I plan on wearing it in the shower and sleeping with it too," he joked of the gold medal draped around his neck.
"I'm going to sleep on it and think about it and see where it holds up against my other medals. I love every one I have and this is just as special."