The home side frittered away a 1-0 half-time advantage before clawing their way back to snatch a point with Ryan Griffiths' 90th-minute goal.
United conceded two second-half goals in between, with Harry Kewell converting a penalty in the 61st minute after Nigel Boogaard was pinged for his ground-level challenge in the box, and Patrick Kisnorbo getting on the end of a wicked Iain Ramsay free kick in the 79th.
"From my position, what I saw on the TV, I felt this was not a penalty," Gombau said.
"I need to check and see exactly what happened ... (but) in the game it is a penalty because the official gave us a penalty.
"The goals came from our mistakes than from their good action.
"The two goals came from a penalty and a foul.
"Of course, in saying this I don't want to say they (Heart) didn't play well - they did their job."
All things given, Gombau believed the deadlock was a fair result given the Reds' patchy play and Heart's second-half gallantry which belied their last-placed standing on the A-League ladder.
"The result is fair because we didn't have a very good game," Gombau said.
"We didn't find the style that we wanted to play.
"They (Melbourne) made it difficult for us.
"I don't want any excuses for this because in the end we had chances to score more goals."
Veteran Griffiths, signed by the Reds earlier this month following a 22-game stint in China with Beijing Baxy, got on the end of Marcelo Carrusca's crisp corner to stun Heart with the equaliser in the final minute of regulation, having subbed into the contest in the 62nd minute.
Griffith's final-ditch salvo came a fortnight after youngster Jordan Elsey's 92nd-minute match-winner which stunned Brisbane Roar at Suncorp Stadium.
For Gombau, the resolve of his players to keep fighting and be looking to score for the full 90-plus minutes is a pleasing sign, as is the off-the-bench impact of level-headed Griffiths.
"He (Griffiths) is an important player," Gombau said.
"He's an experienced player and can help us a lot and bring a lot of solutions.
"We are using him more every day.
"In the last rounds of the season, he will be an important player for us.
"Until the last minute that the game finishes, the ball is in (live).
"Last week we scored in the third minute (against Western Sydney Wanderers); this time we scored in the 90th.
"Every single minute is important."
