Northampton were good value for the win against an Orient side that didn't have the killer touch in front of goal.
Top-scorer Adam Boyd missed a great chance for the O's in the fourth minute when he fired over from a great position after Andy Barcham pulled the ball back.
Boyd went close again in the 11th minute with a snapshot, but it was Northampton who broke the deadlock three minutes later.
Coke, who has been sidelined for most of the season since his arrival from Mansfield, raced onto a flick from Hubertz to beat the advancing Stuart Nelson with a cool finish from the edge of the box.
Orient almost drew level in the 25th minute when Boyd looked certain to score only to be denied by a last-gasp tackle from on-loan defender Mark Little.
Paul Terry almost put the O's back on level terms five minutes before the interval but keeper Mark Bunn reacted well to keep out his deflected effort.
In between, Danny Jackman fired over at the end of an excellent move as Northampton passed the ball around with confidence and Joe Burnell was also just off target after another good move.
Orient picked up the tempo at the start of the second half but despite some neat approach play they were unable to make any impression as the Northampton defensive trio of Little, Brett Johnson and Mark Hughes were outstanding.
Northampton continued to create the better chances with Coke pulling the strings in midfield and Hubertz proving a handful up front.
Jason Crowe headed over from a Daniel Jones free-kick and then Hubertz saw his header from another Jones free-kick saved by Nelson as Cobblers sought the second goal.
It finally arrived in the 78th minute when Hubertz scored from the penalty spot after sending Nelson the wrong way to register his seventh goal of the season after Crowe had been fouled in the box.