The game was delayed for 45 minutes due to a security alert at Kennedy Way in Belfast which had caused traffic disruption for travelling supporters.
The Blues didn't let the disruption faze them though, with Waterworth netting his first of the afternoon five minutes before half time with a neat turn and shot.
The former Glentoran striker's second goal came midway through the second half when he rose at the near post to head home Matthew Tipton's cross and seal a seventh successive win for David Jeffrey's side.
The result leaves the Blues four points clear at the top of the table, although Portadown could close the gap with victory over Mid-Ulster rivals Glenavon on Monday night.
Elsewhere on Saturday, defending champions Cliftonville ended a three game winless streak with a 2-0 victory over Ballinamallard at Ferney Park.
Mallards keeper Alvin Rouse was sent off early on after clattering Joe Gormley who was through on goal, and Liam Boyce played in his strike partner to score the opener from the resulting free kick.
Following a handball from Mark Stafford inside the hosts' penalty area, George McMullan converted the spot-kick in the dying seconds of the game to seal a win which lifts the Reds up to fourth in the table.
Crusaders though still hold bragging rights over their north Belfast rivals after a 4-2 win over Ards saw them move up to third.
It took Stephen Baxter's side just six minutes to get off the mark against the league's bottom side, with Chris Morrow netting from the spot after Greg Hall handled the ball inside the area.
Timmy Adamson made it 2-0 two minutes later when he finished from close-range after Jordan Owens had headed the ball back across goal.
It looked as though the game was done and dusted when Declan Caddell played in Paul Heatley to fire in the Crues third of the afternoon, but to their credit Ards battled back into the game after the break.
Craig McMillen converted an Andrew Mitchell cross to make it 3-1, but Gary McCutcheon made it 4-1 with four minutes remaining.
Ross Arthurs added another consolation in injury time for Ards, who remain rooted to the foot of the table with just six points from 11 games.
In the game at the Ballymena Showgrounds Johnny Taylor spared the home sides blushes as Ballymena United came from two goals down to earn a 2-2 draw with derby rivals Coleraine.
The Bannsiders had Eoin Bradley to thank for their opening goal in the 25th minute, with the Derry GAA star turning the Ballymena defence before firing past Dwayne Nelson.
Stephen Carson netted a superb free kick 8 minutes later, and it looked as though the Sky Blues were on course for their ninth straight defeat at the hands of their north coast rivals.
However Taylor began the comeback with a headed goal from an Allan Teggart corner, and repeated the feat five minutes later to earn a point for his side.
Finally Marcus Kane scored the only goal of the game as Glentoran saw off a game Warrenpoint Town at Stangmore Park.
The midfielder got onto the end of a long throw from Johnny Addis before steering the ball past Johnny Parr in the Warrenpoint goal to send Eddie Patterson's side up to sixth in the table.
Saturday's Danske Bank Premiership results:
Ballinamallard United 0 - 2 Cliftonville
Cliftonville: Joe Gormley (16), George McMullan Goals (45+6 P)
Ballymena United 2 - 2 Coleraine
Ballymena: Johnny Taylor (64, 69)
Coleraine: Eoin Bradley (25), Stephen Carson (33)
Crusaders 4 - 2 Ards
Crusaders: Chris Morrow (6 P), Timmy Adamson (8), Paul Heatley (38), Gary McCutcheon (86)
Ards: Craig McMillen (57), Ross Arthurs (88)
Linfield 2 - 0 Dungannon Swifts
Linfield: Andrew Waterworth (40, 58)
Warrenpoint Town 0 - 1 Glentoran
Glentoran: Marcus Kane (52)