Derek Adams’ players had to battle hard after seeing their visitors, who ended with 10 men, have the better of the first-half chances.
Nevertheless, having scored against Colchester on his loan debut last season, Phillips repeated the trick with half-time looming to give the Shrimps the advantage.
A three-minute spell around the hour mark then saw them take control with Diagouraga doubling their lead before the visitors had Harry Pell sent off.
John O’Sullivan then wrapped up victory with the third goal 10 minutes from time to complete a satisfying day’s work for Morecambe.
Adams had made two changes from the side which drew against Walsall in midweek.
Emergency loanee Jokull Andresson replaced Mark Halstead in goal, while Jordan Slew came in for Aaron Wildig.
A competitive opening saw Stephen Hendrie shoot wide from distance for the Shrimps, while Phillips had a free-kick pushed away by visiting keeper Dean Gerken.
However, it was the visitors who enjoyed the better of the half from an attacking perspective.
Andresson held Cohen Bramall’s header, Noah Chilvers shot wide from long range, while a short corner routine ended with Pell’s effort blocked.
They came closer still on 27 minutes when Jevani Brown found Callum Harriott and his fierce shot struck Andresson’s right-hand post.
Eleven minutes later and the woodwork again came to Morecambe’s rescue, this time Tommy Smith’s close-range header hitting the post.
Andresson also saved efforts from Omar Sowunmi and Kwame Poku before Morecambe took the lead in first-half added time.
Carlos Mendes-Gomes played the ball through and Phillips rounded Gerken before slotting home his ninth of the season.
Half-time saw the Shrimps replace Slew with Diagouraga, a move which paid dividends in the 58th minute when some patient passing play ended with Diagouraga clinically finishing from O’Sullivan’s cross.
Two minutes later and Colchester’s task became harder still when they were reduced to 10 men.
Ryan Cooney took exception to Pell’s challenge and the ensuing altercation ended with a red card for the Colchester midfielder.
Though the visitors shuffled their pack and changed formation as the half progressed, the Shrimps’ numerical advantage meant they were never seriously tested.
They wrapped up victory with 10 minutes remaining when O’Sullivan fired home from Phillips’ pass to make it 10 games without defeat on home soil.
Morecambe: Andresson, Cooney, Lavelle, Knight-Percival, Hendrie, Phillips, Songo’o, O’Sullivan (Price 90), Mendes-Gomes, Slew (Diagouraga 46), Stockton (McAlinden 83). Subs not used: Da Silva Mendes, Pringle, Gibson.
Colchester United: Gerken, Eastman, Sowunmi, Smith, Bramall, Stevenson, Pell, Poku (Welch-Hayes 66), Chilvers, Harriott (Oteh 64), Brown (Folivi 81). Subs not used: George, Senior, Marshall Miranda, Sayer.
Referee: Robert Lewis.
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