Wanjiru made a triumphant US debut in 2hrs 5mins 41secs to defeat Moroccan runner-up Abderrahim Goumi by 23 seconds and shave a second off the old race mark set in 1999 by Morocco's Khalid Khannouchi.
It was the fourth triumph in five career marathons for Wanjiru, who turns 23 next month, and his third major triumph in a row after last August's gold medal effort in China and his London victory six months ago.
Kenya's Vincent Kipruto, who set a Paris Marathon course record of 2:05.47 in just his second career marathon, was third in 2:06:08 with countryman Charles Munyeki fourth in 2:07:07.
Shobukhova took the women's crown in 2:25:55, surging ahead at the final water break to defeat German runner-up Irina Mikitenko, this year's London Marathon winner, by 36 seconds with Russian Lidya Grigoryeva third in 2:26:47.
Runners wore stocking caps and gloves as a field of 45,000 braved chilly conditions in the "Windy City" nine days after it lost out to Rio de Janeiro in a bid to host the 2016 Summer Olympics.
Wanjiru was 31 seconds off the personal best of 2:05:10 he set to win in April in London and 71 seconds off the world record set last year in Berlin by Ethiopia's Haile Gebrselassie.
An elite men's group of eight took the lead after 15 kilometres but near the mid-point the pack had thinned under a withering stride, four seconds under world record pace at 10 miles.
The midway lead was an all-Kenyan affair between Kipruto, Wanjiru and Charles Munyeki after the drop off of Kenyan pacemaker Patrick Ivuti, who led the stars to the halfway mark three seconds off world record pace at 1:02:01.
The front trio then slowed and began a tactical race, allowing Goumri to close the gap as Wanjiru made his move 20 minutes from the end, surging ahead at 35km to see if his rivals could answer the call.
They could not and Wanjiru stretched his edge seemingly with every stride as his compatriots fell behind hard-closing Goumri.
On the women's side, Ethiopia's Teyba Erkesso, who won this year's Houston Marathon in 2:24:18, pushed ahead after 15 kilometres before being chased down by five rivals who picked up their own pace.
At the midpoint, Erkesso led at 1:15:04 with Mikitenko, Shobukhova, two-time Chicago winner Berhane Adere of Ethiopia, 2008 champion Grigoryeva and Japan's Mizuho Nasukawa on her heels.
That pack began a tactical run until with three miles remaining it had withered to the podium finishers and Erkesso, who settled for fourth by nine seconds.
Shobukova, 31, made her move after a quick fluid grab at the last station and her rivals were unable to answer the challenge, although she was 91 seconds off her personal best and 8:37 off British star Paula Radcliffe's course record.
Mikitenko, 37, who was second in 2:26:31, dedicated her race to her late father.
Adere was fifth in 2:28:38, failing to become the first three-time Chicago winner.
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