Substitute Deeney beat Andy Lonergan with a low shot to give the Hornets a 4-3 victory in a breathtaking contest.
Clough's second equaliser with five minutes left brought the sides level at 3-3 after Joel Ekstrand had put Watford back in control.
The Hornets had taken the lead through Odion Ighalo and although goals from Clough and Adam Le Fondre had turned the tide, the visitors went back in front thanks to strikes from Almen Abdi and Ekstrand before the late drama.
There was another thriller at Bloomfield Road, where David Ferguson's stoppage-time equaliser capped a pulsating second half which saw nine-man Blackpool earn a dramatic 4-4 draw against Nottingham Forest.
A win for the Seasiders would have moved them off the foot of the table, and they were on course for just their fifth of the season when Gary Madine put them ahead.
Andrea Orlandi added a second but Forest scored twice in two minutes through Dexter Blackstock and Gary Gardner to draw level.
Steve Davies restored the home side's lead before Forest midfielder Henri Lansbury tucked home a spot-kick - the concession of which saw Tom Aldred red-carded.
Darren O'Dea was then stretchered off to leave Blackpool two men light and Chris Burke thought he had won it for the visitors with a goal five minutes into added time
But Ferguson headed home to salvage a stunning point for the hosts
Bournemouth climbed back to the top of the table after a 1-1 draw at home to Huddersfield, who had James Vaughan to thank for cancelling out Yann Kermorgant's opener
Daryl Murphy scored twice to bring Ipswich to within two points of the automatic promotion places as they secured a deserved 2-1 win over Fulham, who netted through Ross McCormack.
Norwich's promotion challenge continued to gather pace as they downed Wolves 2-0 at Carrow Road to make it three straight league wins, Bradley Johnson and Lewis Grabban the goalscorers
Alex Mowatt scored the only goal of the game as Leeds beat Millwall 1-0 to move into the top half.
Guy Luzon celebrated his first victory as Charlton boss as his side beat play-off chasing Brentford 3-0 thanks to goals from Johann Gudmundsson, Igor Vetokele and Frederic Bulot.
Sheffield Wednesday and Brighton drew 0-0 at Hillsborough.
Source : PA
Source: PA