An own goal from Michel Breuer and an Alan Shearer free-kick in the first half at St James' Park sealed the Magpies' passage and set up a meeting with Greek side Olympiakos in the next round.
The visitors made a bright start, before Breuer's intervention gave the Magpies the lead on the night. The defender attempted to clear Laurent Robert's tenth minute cross, but managed only to divert the ball past Brian Vandenbussche and into the net.
Shola Ameobi went close to doubling the lead before skipper Shearer did so with 25 minutes on the clock.
Kieron Dyer was fouled 25 yards from goal and from the resulting free-kick Robert rolled the ball to Shearer and he rifled a low shot into the corner of the net, despite the best efforts of Vandenbussche.
Shortly afterwards Ameobi's header from another Robert delivery grazed the outside of the post.
Heerenveen rarely threatened up to half-time, with Arnold Bruggink firing a rare chance just wide of the far post.
The Magpies brought on Jermaine Jenas for Dyer at the interval, with the opening minutes of the second half seeing little action in either goalmouth.
Another sub, James Milner, almost made it 3-0 midway through the second period, but with ten minutes to play Heerenveen were handed a lifeline.
Newcastle United 2 Heerenveen 1
Ameobi inexplicably handled following a corner and Bruggink sent Shay Given the wrong way to make the score 2-1 on the night and 4-2 on aggregate.
The goalscorer was immediately replaced by Victor Sikora and the former Ajax winger almost netted an equaliser, being denied by Ameobi's header away from close to the goal-line.
However, despite Milner passing up a good late chance, Graeme Souness' side had done more than enough to ensure a place in the last 16 of the competition.
The goalscorer was immediately replaced by Victor Sikora and the former Ajax winger almost netted an equaliser, being denied by Ameobi's header away from close to the goal-line.
However, despite Milner passing up a good late chance, Graeme Souness' side had done more than enough to ensure a place in the last 16 of the competition.