Dunfermline goalkeeper Chris Smith gifted Motherwell the opening goal when he let Michael Higdon's weak shot slip through his grasp in the 64th minute.
Henrik Ojamaa then doubled the visitors' lead when he rocketed a shot beyond the helpless keeper six minutes later.
Victory for Motherwell moves them within three points of Rangers in second place while Dunfermline are now four points adrift at the foot of table.
Dunfermline began the game hoping to record their first home win of the season and Liam Buchanan tested Darren Randolph after two minutes.
Motherwell had a chance of their own just a minute later when Ojamaa struck wide of the target after Alex Keddie blocked Jamie Murphy's long-range drive.
Randolph produced an excellent stop to keep out Martin Hardie's stinging effort and Shaun Hutchinson made a crucial tackle at the feet of Ryan Thomson as the hosts enjoyed a bright opening spell.
The visitors created their best chance of the first half just before the half-hour mark.
Tom Hateley's surging run ended with a smart pass to Murphy who laid the ball to Higdon, but the striker's tame effort was gathered comfortably by Smith.
Thomson saw his effort from the edge of the box easily dealt with by Randolph as Dunfermline looked to end the first half on a high, although at the other end Smith had to be alert to tip Omar Daley's dipping cross onto the roof of his goal just before the interval.
Both sides made changes at the interval, Paul Willis replaced Joe Cardle for Dunfermline while Chris Humphrey was introduced in place of Omar Daley for the visitors.
A lightening quick break from a Dunfermline corner almost led to Motherwell grabbing the lead.
Ojamaa released Murphy who denied by an excellent last-ditch tackle by Alex Keddie.
Keddie came to the Dunfermline's rescue again two minutes later when he diverted Ojamaa's shot away for a corner.
Hutchinson deflected Buchanan's fizzing drive wide of the target just before the hour mark and Steven Hammell was forced into a good clearing header from Willis' corner.
An error from Dunfermline keeper Smith led to Motherwell opening the scoring.
Higdon connected with Ojamaa's cross at the front post and his shot somehow slipped underneath Smith and into the net.
Austin McCann received a booking for hauling down Humphrey after 68 minutes and the Jamaican was involved again two minutes later as Motherwell stretched their lead - sliding the ball to Ojamaa who lashed the ball beyond Smith.
Dunfermline made their second change of the match when Andy Barrowman replaced Martin Hardie with 15 minutes remaining.
A vital header at the back-post by Andy Dowie prevented Tim Clancy from getting on the end of Hateley's dangerous free-kick as the visitors looked to inflict further misery on their opponents.
Murphy flashed a shot across the face of Smith's goal with seven minutes remaining as Motherwell continued to control proceedings.
And the 23-year-old then fired over after running on to Higdon's knockdown in the final minute of the match.