Stevenage's 13-game unbeaten run came to an end as Leyton Orient won a fiery encounter at Broadhall Way.
Lee Cook scored the only goal after 15 minutes when he cut in from the right and curled a shot into the top corner from 20 yards out.
Orient went down to 10 men when defender Ben Chorley was sent off in first-half injury-time for a clash with Chris Beardsley.
But Boro had Chuks Aneke dismissed for a high challenge on Terrell Forbes.
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Stevenage manager graham Westley told BBC Three Counties Radio:
"It was a very uncharacteristic performance. We looked tired physically and mentally.
"We looked like a side that had done too much winning and we certainly didn't put in enough to create the domination we usually do.
"It's a backwards step for sure and one we need to use in a positive way."
Leyton Orient manager Russell Slade told BBC London 94.9:
"We had to show a different side of us today. It's not an easy place to come and get a result but I thought we mixed it up really well and thoroughly deserved to be in front.
"The decision looks really harsh for a straight red to me and that could've been a turning point in the game. But I'm glad it wasn't and we managed to get the three points.
"It's difficult to pick a man out because they were all fantastic but I have to say every time there was danger in there Scottie Cuthbert was absolutely awesome. It was a fantastic performance from a centre half."