Sri Lanka entered the final day 347 runs behind the West Indies after trailing by 376 when the home team declared its second innings on Thursday at 280-4.
The experienced opener scored a patient 85 which, along with half-centuries from Kyle Mayers and Jason Holder, allowed West Indies to declare at 280/4.
Only 40.3 overs were bowled on a day that saw four rain interruptions.
Dinesh Chandimal and Dhananjaya de Silva put in an unbroken fourth-wicket partnership of 59 as Sri Lanka end the day at 136-3, 218 runs behind.
The West Indies captain's stands of 71 with Kyle Mayers, 51 with Holder, and an unbeaten 65 with Rakheem Cornwall ensured they finished the first day on top
Windies cricket chief Ricky Skerritt added that the board's debt has reduced to a third in his tenure.
When stumps were drawn early, the West Indies were 236-4, with Bonner 113 not out and Jason Holder on 13.
Starting 102 runs behind on the first innings, Sri Lanka reached 476 in its second innings for a lead of 374.
Last year in July, England and West Indies had restarted international cricket amid the COVID-19 pandemic with a three-match Test series.
Cornwall was 60 not out at stumps, the first Antiguan to score a Test half-century at the Sir Vivian Richards Stadium.
Holder's spell broke the back of the innings and he then ripped through the lower half of the batting.
The Windies new Test captain celebrated his first Test in charge against Sri Lanka as he ran out Oshada Fernandes with a direct him as former skipper Jason Holder picks five-for.
The entire process, including the announcement of the host island nations, is expected to get over next month.
West Indies batsman Chris Gayle, in a video message, thanked PM Modi for India's donation of COVID-19 vaccines to Jamaica.
Yuvraj finished with 49 off 20 deliveries that included a four and 6 sixes.
Live Streaming Road Safety World Series India Legends vs West Indies Legends: Follow ball-by-ball updates from IND-L vs WI-L Live Online
Gunathilaka has been reprimanded for breaching Level 1 of the ICC Code of Conduct during the same match for giving a send-off to Nicholas Pooran.
The victory also gave West Indies 30 valuable points and moved them up to sixth position in the International Cricket Council's Super League table in the run for the 2023 World Cup.
The third and final ODI played in Antigua was briefly halted during the 38th over of the first innings when a swarm of bees forced players to lie down on the ground.
Holder, who has been replaced as captain by Kraigg Brathwaite for the Test series, missed the tour of Bangladesh along with batsman Darren Bravo, who too returns to the squad.
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