Chebet won in two hours, six minutes and 51 seconds to top the first all-Kenyan podium since 2012, beating 2019 Boston winner Lawrence Cherono by 30 seconds with defending champion Benson Kipruto third in 2:07:27.
"I'm extremely proud," Chebet said through a translator. "I knew I had it in my legs to win."
Jepchirchir, last year's New York Marathon champion, won her Boston debut by edging Ethiopia's Ababel Yeshaneh in the final strides, taking her fifth victory in a row since 2019 in 2:21:01.
That was good enough to defeat Yeshaneh by four seconds with Kenya's Mary Ngugi third in 2:21:32.
As they battled into the final mile, Jepchirchir made three pass attempts but Yeshaneh countered each. The Kenyan made her final move down the stretch and surged in the last 100 meters for the triumph.
"When I arrived to 41km, I knew was going to win the race," Jepchirchir said. "I was just keeping the energy for the finishing. Ababel was so strong. For me, it was just keeping my energy for the finishing kick.
"I just believed in myself. I usually have hope. When you see the tape for finishing, that's when the strength comes."
Jepchirchir ranked Boston among her greatest victories.
"It means a lot to me," she said. "I believe in myself more. I still have more victories to come."
- Full field -
The famed 26.2-mile race returned to its traditional date on the third Monday in April after being canceled in 2020 and contested in October last year due to Covid-19 concerns.
A full field of 30,000 competitors took part with Covid-19 vaccinations required for entry into the event.
Chebet, 33, was the 2020 world leader from a Valencia Marathon victory in 2:03:00. He was fourth in last year's London Marathon.
A lead pack of about 20 men reached the halfway mark together and 15 remained tight at the front through 21 miles, with Chebet, who didn't finish in 2018 in his only other Boston start, making his move just after that with a 4:27 mile.
By mile 23 he had left behind the field, but Cherono and Kipruto kept the pressure on Chebet into the final stretch.
Kenyan Albert Korir, last year's New York Marathon winner, was sixth in 2:08:50 and compatriot Geoffrey Kamworor, a two-time New York winner, was 18th.
Japan's Yuki Kawauchi, the 2018 Boston champion, was 20th while 2016 winner and 2021 runner-up Lemi Berhanu of Ethiopia was 11th.
On the women's side, former Boston, London and New York champion Edna Kiplagat of Kenya was fourth in 2:21:40 while 2021 London winner Joyciline Jepkosgei of Kenya was seventh.
Jepchirchir and Jepkosgei pushed the pace on a climb after half an hour to trim the lead pack to about a dozen and after a few miles the only rival with them was Yeshaneh, a 2019 Chicago runner-up and former world half-marathon record holder.
American Daniel Romanchuk won the men's wheelchair title for a second time and Swiss Manuela Schar won the women's wheelchair crown.