Liverpool took the lead in the match after four minutes through John Aldridge, and held onto that lead until the ninetieth minute, when Everton substitute Stuart McCall equalised, and a pitch invasion by Everton fans ensued. McCall had scored just once for Everton before the FA Cup final, having joined them from Bradford City at the start of the season.
McCall's goal was the last kick of the 90 minutes and the match went into extra time. On 95 minutes, Liverpool substitute Ian Rush scored with a half-volley on the turn to give Liverpool a 2–1 lead. Everton again equalised five minutes later when McCall scored his second, chesting and volleying past Bruce Grobbelaar and into the corner of the net. However, Rush – who had scored twice in Liverpool's 3–1 win in the first Merseyside derby Final three years earlier – scored his second goal in the 104th minute, with a header from a floated John Barnes cross.
Liverpool had continued their domination of the English game (they were league champions in 1988 and runners-up in 1987), but Everton had declined since their 1987 title triumph and finished sixth in the league in 1989.
UEFA voted for the ban on English clubs in European competitions to continue for a fifth season, ruling out Liverpool's hopes of competing in the Cup Winners' Cup – although they were still in contention for the league title at this stage, and ultimately were only deprived of the title (and a unique second double) by a last-gasp goal in their final game of the season. Had the ban on English clubs in European competitions been lifted and Liverpool had won the league, Everton would have been able to compete in the Cup Winners' Cup.
Liverpool striker Ian Rush had now scored four goals in FA Cup finals (both two-goal hauls against Everton) and was one of 11 players (five for Liverpool) to have featured in both of the all-Merseyside FA Cup finals. Stuart McCall made FA Cup history when he became the first substitute to score 2 goals in an FA Cup final. However, Ian Rush matched the feat two minutes later.