The away side brushed off the absence of the suspended Mario Balotelli to cut the gap on third-placed Lyon to five points, while Guingamp remained four points adrift of the relegation play-off spot, having conceded at least 10 more goals than every other team in the French top flight.
Marseille took less than four minutes to take the lead as Dimitri Payet’s right-wing cross fell kindly for Luiz Gustavo to lash the ball into the net from close range.
The visitors’ second goal was gifted to them by the hapless home defence five minutes before half-time, as Lucas Ocampos drifted into the box totally unmarked to send a header bouncing past goalkeeper Marc-Aurele Caillard from Florian Thauvin’s ball across the middle.
Guingamp were in desperate need of points to boost their survival bid, and half-time substitute Yeni Atito N’Gbakoto halved the deficit 11 minutes after the restart.
But fourth-placed Marseille wrapped up a second straight win in injury-time as Valere Germain lashed an excellent volley in off the crossbar.